Phylogeny of elasmobranchs based on LSU and SSU ribosomal RNA genes

Morphology and phylogenetic implications of the inclinatores dorsales for the galeomorph sharks (Chondrichthyes: Elasmobranchii)

Elasmobranchs have been studied in anatomical terms for nearly 200 years, but several elements of their anatomy, such as the dorsal fin musculature, have not been completely addressed and still lack detailed descriptions. In this context, the present study investigates the anatomical variation of the muscles inclinatores dorsales across galeomorph sharks, shedding new light on their evolution. We have observed that the inclinatores dorsales have two distinct components, being composed of a profundus and a superficialis component. Additionally, we have uncovered, through an anatomical comparative analysis, that the variation present in these muscles is considerably greater than previously considered, indicating some characteristics never described before, for instance the presence or absence of the inclinatores dorsales at the free rear tip of the first dorsal fin. Moreover, our findings for the inclinatores dorsales are different from their previous interpretation in the context of the hypnosqualean hypothesis, reinforcing the need for a reevaluation of previous morphological characters. Lastly, we discuss our findings in relation to the most recent interrelationships of elasmobranchs.

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.

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.

Branching patterns of the afferent branchial arteries and their phylogenetic significance in rays (Batoidea)

Rays of the superorder Batoidea comprise the most diverse group of chondrichthyans in terms of valid species and morphological disparity. Up to the present little agreement is observed in studies based on morphological and molecular data focused on uncovering the interrelationships within Batoidea. Morphology-based phylogenies of batoids have not included characters related to the afferent branchial arteries, and little is known about the variation in this anatomical complex in rays. Herein, representatives of 32 genera from 19 families currently recognized of rays were examined as well as some shark taxa. Seven new characters are proposed and tested in two different analyses, one on their own and in the other they were added to the morphological data matrix of the most recent analysis of interrelationships within Batoidea. The arrangement of afferent branchial arteries differs mainly among orders and families of batoids. The absence of a common trunk from which the three posteriormost afferent arteries branch is interpreted as a synapomorphy for Myliobatiformes and the presence of a coronary cranial artery as an autapomorphy for Mobula hypostoma. A close spatial relationship between the second and third afferent arteries within the common branch from the ventral aorta is proposed as a synapomorphy for Rajiformes with a secondary modification in Sympterygia. Data about patterns in afferent branchial arteries in additional taxa such as Squaliformes and Chimaeriformes are needed to better understand the evolution of this character complex among chondrichthyans.

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.

Cerebrovascular β-dystroglycan immunoreactivity in vertebrates: not detected in anurans and in the teleosts Ostariophysi and Euteleostei

The aim of the present paper was to check for the presence of cerebrovascular dystroglycan in vertebrates, because dystroglycan, which is localized in the vascular astroglial end-feet, has a pivotal function in glio-vascular connections. In mammalian brains, the immunoreactivity of β-dystroglycan subunit delineates the vessels. The results of the present study demonstrate similar patterns in other vertebrates, except for anurans and the teleost groups Ostariophysi and Euteleostei. In this study, we investigated 1 or 2 representative species of the main groups of Chondrichthyes, teleost and non-teleost ray-finned fishes, urodeles, anurans, and reptiles. We also investigated 5 mammalian and 3 bird species. Animals were obtained from breeders or fishermen. The presence of β-dystroglycan was investigated immunohistochemically in free-floating sections. Pre-embedding electron microscopical immunohistochemistry on Heterodontus japonicus shark brains demonstrated that in Elasmobranchii, β-dystroglycan is also localized in the perivascular glial end-feet despite the different construction of their blood-brain barrier. The results indicated that the cerebrovascular β-dystroglycan immunoreactivity disappeared separately in anurans, and in teleosts, in the latter group before its division to Ostariophysi and Euteleostei. Immunohistochemistry in muscles and western blots from brain homogenates, however, detected the presence of β-dystroglycan, even in anurans and all teleosts. A possible explanation is that in the glial end-feet, β-dystroglycan is masked in these animals, or disappeared during adaptation to the freshwater habitat.

New Carcharhiniform Sharks (Chondrichthyes, Elasmobranchii) from the Early to Middle Eocene of Seymour Island, Antarctic Peninsula

Seymour Island, Antarctic Peninsula, is known for its wealth of fossil remains. This island provides one of the richest fossiliferous Paleogene sequences in the world. Chondrichthyans seemingly dominate this Eocene marine fauna and offer a rare insight into high-latitude faunas during the Palaeogene. So far, only a few isolated teeth of carcharhinid sharks have been reported from Seymour Island. Bulk sampling in the well-exposed La Meseta and Submeseta formations yielded new and abundant chondrichthyan material, including numerous teeth of carcharhinid and triakid sharks. Here, we present a reevaluation of the previously described carcharhinid remains and a description of new taxa: Meridiogaleus cristatus, gen. et sp. nov., Kallodentis rythistemma, gen. et sp. nov., Abdounia richteri, sp. nov., and Abdounia mesetae, sp. nov. The carcharhiniforms Mustelus sp. and Galeorhinus sp. are reported based on rare material, whereas teeth previously assigned to Scoliodon represent a nomen dubium.

Origins of the Greenland shark (Somniosus microcephalus): Impacts of ice-olation and introgression

Herein, we use genetic data from 277 sleeper sharks to perform coalescent‐based modeling to test the hypothesis of early Quaternary emergence of the Greenland shark (Somniosus microcephalus) from ancestral sleeper sharks in the Canadian Arctic‐Subarctic region. Our results show that morphologically cryptic somniosids S. microcephalus and Somniosus pacificus can be genetically distinguished using combined mitochondrial and nuclear DNA markers. Our data confirm the presence of genetically admixed individuals in the Canadian Arctic and sub‐Arctic, and temperate Eastern Atlantic regions, suggesting introgressive hybridization upon secondary contact following the initial species divergence. Conservative substitution rates fitted to an Isolation with Migration (IM) model indicate a likely species divergence time of 2.34 Ma, using the mitochondrial sequence DNA, which in conjunction with the geographic distribution of admixtures and Pacific signatures likely indicates speciation associated with processes other than the closing of the Isthmus of Panama. This time span coincides with further planetary cooling in the early Quaternary period followed by the onset of oscillating glacial‐interglacial cycles. We propose that the initial S. microcephalus–S. pacificus split, and subsequent hybridization events, were likely associated with the onset of Pleistocene glacial oscillations, whereby fluctuating sea levels constrained connectivity among Arctic oceanic basins, Arctic marginal seas, and the North Atlantic Ocean. Our data demonstrates support for the evolutionary consequences of oscillatory vicariance via transient oceanic isolation with subsequent secondary contact associated with fluctuating sea levels throughout the Quaternary period—which may serve as a model for the origins of Arctic marine fauna on a broad taxonomic scale.

Functional analysis of the musculo-skeletal system of the gill apparatus in Heptranchias perlo (Chondrichthyes: Hexanchidae)

Musculo-skeletal morphology is an indispensable source for understanding functional adaptations. Analysis of morphology of the branchial apparatus of Hexanchiform sharks can provide insight into aspects of their respiration that are difficult to observe directly. In this study, I compare the structure of the musculo-skeletal system of the gill apparatus of Heptranchias perlo and Squalus acanthias in respect to their adaptation for one of two respiratory mechanisms known in sharks, namely, the active two-pump (oropharyngeal and parabranchial) ventilation and the ram-jet ventilation. In both species, the oropharyngeal pump possesses two sets of muscles, one for compression and the other for expansion. The parabranchial pump only has constrictors. Expansion of this pump occurs only due to passive elastic recoil of the extrabranchial cartilages. In Squalus acanthias the parabranchial chambers are large and equipped by powerful superficial constrictors. These muscles and the outer walls of the parabranchial chambers are much reduced in Heptranchias perlo, and thus it likely cannot use this pump. However, this reduction allows for vertical elongation of outer gill slits which, along with greater number of gill pouches, likely decreases branchial resistance and, at the same time, increases the gill surface area, and can be regarded as an adaptation for ram ventilation at lower speeds.

Fin modules: an evolutionary perspective on appendage disparity in basal vertebrates

BACKGROUND

Fishes are extremely speciose and also highly disparate in their fin configurations, more specifically in the number of fins present as well as their structure, shape, and size. How they achieved this remarkable disparity is difficult to explain in the absence of any comprehensive overview of the evolutionary history of fish appendages. Fin modularity could provide an explanation for both the observed disparity in fin configurations and the sequential appearance of new fins. Modularity is considered as an important prerequisite for the evolvability of living systems, enabling individual modules to be optimized without interfering with others. Similarities in developmental patterns between some of the fins already suggest that they form developmental modules during ontogeny. At a macroevolutionary scale, these developmental modules could act as evolutionary units of change and contribute to the disparity in fin configurations. This study addresses fin disparity in a phylogenetic perspective, while focusing on the presence/absence and number of each of the median and paired fins.

RESULTS

Patterns of fin morphological disparity were assessed by mapping fin characters on a new phylogenetic supertree of fish orders. Among agnathans, disparity in fin configurations results from the sequential appearance of novel fins forming various combinations. Both median and paired fins would have appeared first as elongated ribbon-like structures, which were the precursors for more constricted appendages. Among chondrichthyans, disparity in fin configurations relates mostly to median fin losses. Among actinopterygians, fin disparity involves fin losses, the addition of novel fins (e.g., the adipose fin), and coordinated duplications of the dorsal and anal fins. Furthermore, some pairs of fins, notably the dorsal/anal and pectoral/pelvic fins, show non-independence in their character distribution, supporting expectations based on developmental and morphological evidence that these fin pairs form evolutionary modules.

CONCLUSIONS

Our results suggest that the pectoral/pelvic fins and the dorsal/anal fins form two distinct evolutionary modules, and that the latter is nested within a more inclusive median fins module. Because the modularity hypotheses that we are testing are also supported by developmental and variational data, this constitutes a striking example linking developmental, variational, and evolutionary modules.

Revision of Eocene Antarctic carpet sharks (Elasmobranchii, Orectolobiformes) from Seymour Island, Antarctic Peninsula

Seymour Island, Antarctic Peninsula, was once called the 'Rosetta Stone' of Southern Hemisphere palaeobiology, because this small island provides the most complete and richly fossiliferous Palaeogene sequence in Antarctica. Among fossil marine vertebrate remains, chondrichthyans seemingly were dominant elements in the Eocene Antarctic fish fauna. The fossiliferous sediments on Seymour Island are from the La Meseta Formation, which was originally divided into seven stratigraphical levels, TELMs 1-7 (acronym for Tertiary Eocene La Meseta) ranging from the upper Ypresian (early Eocene) to the late Priabonian (late Eocene). Bulk sampling of unconsolidated sediments from TELMs 5 and 6, which are Ypresian (early Eocene) and Lutetian (middle Eocene) in age, respectively, yielded very rich and diverse chondrichthyan assemblages including over 40 teeth of carpet sharks representing two new taxa, Notoramphoscyllium woodwardi gen. et sp. nov. and Ceolometlaouia pannucae gen. et sp. nov. Two additional teeth from TELM 5 represent two different taxa that cannot be assigned to any specific taxon and thus are left in open nomenclature. The new material not only increases the diversity of Eocene Antarctic selachian faunas but also allows two previous orectolobiform records to be re-evaluated. Accordingly, Stegostoma cf. faciatum is synonymized with Notoramphoscyllium woodwardi gen. et sp. nov., whereas Pseudoginglymostoma cf. brevicaudatum represents a nomen dubium. The two new taxa, and probably the additional two unidentified taxa, are interpreted as permanent residents, which most likely were endemic to Antarctic waters during the Eocene and adapted to shallow and estuarine environments.

Visual resolution and contrast sensitivity in two benthic sharks

Sharks have long been described as having 'poor' vision. They are cone monochromats and anatomical estimates suggest they have low spatial resolution. However, there are no direct behavioural measurements of spatial resolution or contrast sensitivity. This study estimates contrast sensitivity and spatial resolution of two species of benthic sharks, the Port Jackson shark, Heterodontus portusjacksoni, and the brown-banded bamboo shark, Chiloscyllium punctatum, by recording eye movements in response to optokinetic stimuli. Both species tracked moving low spatial frequency gratings with weak but consistent eye movements. Eye movements ceased at 0.38 cycles per degree, even for high contrasts, suggesting low spatial resolution. However, at lower spatial frequencies, eye movements were elicited by low contrast gratings, 1.3% and 2.9% contrast in H portusjacksoni and C. punctatum, respectively. Contrast sensitivity was higher than in other vertebrates with a similar spatial resolving power, which may reflect an adaptation to the relatively low contrast encountered in aquatic environments. Optokinetic gain was consistently low and neither species stabilised the gratings on their retina. To check whether restraining the animals affected their optokinetic responses, we also analysed eye movements in free-swimming C. punctatum We found no eye movements that could compensate for body rotations, suggesting that vision may pass through phases of stabilisation and blur during swimming. As C. punctatum is a sedentary benthic species, gaze stabilisation during swimming may not be essential. Our results suggest that vision in sharks is not 'poor' as previously suggested, but optimised for contrast detection rather than spatial resolution.

Re-evaluation of batoid pectoral morphology reveals novel patterns of diversity among major lineages

Batoids (Chondrichthyes: Batoidea) are a diverse group of cartilaginous fishes which comprise a monophyletic sister lineage to all neoselachians or modern sharks. All species in this group possess anteroposteriorly expanded-pectoral fins, giving them a unique disc-like body form. Reliance on pectoral fins for propulsion ranges from minimal (sawfish) to almost complete dependence (skates and rays). A recent study on the diversity of planform pectoral fin shape in batoids compared overall patterns of morphological variation within the group. However, inconsistent pectoral homology prevented the study from accurately representing relationships within and among major batoid taxa. With previous work in mind, we undertook an independent investigation of pectoral form in batoids and evaluated the implications of shape diversity on locomotion and lifestyle, particularly in the skates (Rajoidei) and rays (Myliobatoidei). We used geometric morphometrics with sliding semilandmarks to analyze pectoral fin outlines and also calculate fin aspect ratios (AR), a functional trait linked to locomotion. In agreement with previous work, our results indicated that much of the evolution of batoid pectoral shape has occurred along a morphological axis that is closely related to AR. For species where kinematic data were available, both shape and AR were associated with swimming mode. This work further revealed novel patterns of shape variation among batoids, including strong bimodality of shape in rays, an intermediate location of skate species in the morphospace between benthic/demersal and pelagic rays, and approximately parallel shape trajectories in the benthic/demersal rays and skates. Finally, manipulation of landmarks verified the need for a consistent and accurate definition of homology for the outcome and efficacy of analyses of pectoral form and function in batoids.

Complete mitochondrial DNA genome of bonnethead shark, Sphyrna tiburo, and phylogenetic relationships among main superorders of modern elasmobranchs

Elasmobranchs are one of the most diverse groups in the marine realm represented by 18 orders, 55 families and about 1200 species reported, but also one of the most vulnerable to exploitation and to climate change. Phylogenetic relationships among main orders have been controversial since the emergence of the Hypnosqualean hypothesis by Shirai (1992) that considered batoids as a sister group of sharks. The use of the complete mitochondrial DNA (mtDNA) may shed light to further validate this hypothesis by increasing the number of informative characters. We report the mtDNA genome of the bonnethead shark Sphyrna tiburo, and compare it with mitogenomes of other 48 species to assess phylogenetic relationships. The mtDNA genome of S. tiburo, is quite similar in size to that of congeneric species but also similar to the reported mtDNA genome of other Carcharhinidae species. Like most vertebrate mitochondrial genomes, it contained 13 protein coding genes, two rRNA genes and 22 tRNA genes and the control region of 1086 bp (D-loop). The Bayesian analysis of the 49 mitogenomes supported the view that sharks and batoids are separate groups.

Molecular organization of the 5S rDNA gene type II in elasmobranchs

The 5S rDNA gene is a non-coding RNA that can be found in 2 copies (type I and type II) in bony and cartilaginous fish. Previous studies have pointed out that type II gene is a paralog derived from type I. We analyzed the molecular organization of 5S rDNA type II in elasmobranchs. Although the structure of the 5S rDNA is supposed to be highly conserved, our results show that the secondary structure in this group possesses some variability and is different than the consensus secondary structure. One of these differences in Selachii is an internal loop at nucleotides 7 and 112. These mutations observed in the transcribed region suggest an independent origin of the gene among Batoids and Selachii. All promoters were highly conserved with the exception of BoxA, possibly due to its affinity to polymerase III. This latter enzyme recognizes a dT4 sequence as stop signal, however in Rajiformes this signal was doubled in length to dT8. This could be an adaptation toward a higher efficiency in the termination process. Our results suggest that there is no TATA box in elasmobranchs in the NTS region. We also provide some evidence suggesting that the complexity of the microsatellites present in the NTS region play an important role in the 5S rRNA gene since it is significantly correlated with the length of the NTS.

Fatal Fusarium solani species complex infections in elasmobranchs: the first case report for black spotted stingray (Taeniura melanopsila) and a literature review

Fusarium species are environmental saprophytic fungi. Among the many Fusarium species, members of the Fusarium solani species complex (FSSC) are the most prevalent and virulent in causing human and animal infections. In this study, we describe the first case of fatal FSSC infection in a black spotted stingray and three concomitant infections in scalloped hammerhead sharks. In the stingray, cutaneous lesions were characterised by ulcers and haemorrhage of the ventral pectoral fin, or 'ray', especially around the head; while cutaneous lesions in the sharks were characterised by ulcers, haemorrhage, as well as white and purulent exudates at the cephalic canals of the cephalofoil and lateral line. Histological sections of the cutaneous lesions revealed slender (1-4 μm in diameter), branching, septate fungal hyphae. Internal transcribed spacer region and 28S nrDNA sequencing of the fungal isolates from the fish showed two isolates were F. keratoplasticum (FSSC 2) and the other two were FSSC 12. Environmental investigation revealed the FSSC strains isolated from water and biofilms in tanks that housed the elasmobranchs were also F. keratoplasticum and FSSC 12. Fusarium is associated with major infections in elasmobranchs and FSSC 12 is an emerging cause of infections in marine animals. DNA sequencing is so far the most reliable method for accurate identification of Fusarium species.

Development and evolution of dentition pattern and tooth order in the skates and rays (batoidea; chondrichthyes)

Shark and ray (elasmobranch) dentitions are well known for their multiple generations of teeth, with isolated teeth being common in the fossil record. However, how the diverse dentitions characteristic of elasmobranchs form is still poorly understood. Data on the development and maintenance of the dental patterning in this major vertebrate group will allow comparisons to other morphologically diverse taxa, including the bony fishes, in order to identify shared pattern characters for the vertebrate dentition as a whole. Data is especially lacking from the Batoidea (skates and rays), hence our objective is to compile data on embryonic and adult batoid tooth development contributing to ordering of the dentition, from cleared and stained specimens and micro-CT scans, with 3D rendered models. We selected species (adult and embryonic) spanning phylogenetically significant batoid clades, such that our observations may raise questions about relationships within the batoids, particularly with respect to current molecular-based analyses. We include developmental data from embryos of recent model organisms Leucoraja erinacea and Raja clavata to evaluate the earliest establishment of the dentition. Characters of the batoid dentition investigated include alternate addition of teeth as offset successional tooth rows (versus single separate files), presence of a symphyseal initiator region (symphyseal tooth present, or absent, but with two parasymphyseal teeth) and a restriction to tooth addition along each jaw reducing the number of tooth families, relative to addition of successor teeth within each family. Our ultimate aim is to understand the shared characters of the batoids, and whether or not these dental characters are shared more broadly within elasmobranchs, by comparing these to dentitions in shark outgroups. These developmental morphological analyses will provide a solid basis to better understand dental evolution in these important vertebrate groups as well as the general plesiomorphic vertebrate dental condition.

Population structure of Squatina guggenheim (Squatiniformes, Squatinidae) from the south-western Atlantic Ocean

Population genetic analyses based on both mitochondrial cytochrome b and the internal transcribed spacer 2 of recombinant (r)DNA genes were implemented to examine hypotheses of population differentiation in the angular angel shark Squatina guggenheim, one of the four most-widespread endemic species inhabiting coastal ecosystems in the south-western Atlantic Ocean. A total of 82 individuals of S. guggenheim from 10 sampling sites throughout the Río de la Plata mouth, its maritime front, the outer shelf at the subtropical confluence and the coastal areas of the south-west Atlantic Ocean, were included. The analysis of molecular variance (AMOVA) based on the second internal transcribed spacer (its-2) region supports that the samples from the outer shelf represent an isolated group from other sites. Historical gene flow in a coalescent-based approach revealed significant immigration and emigration asymmetry between sampling sites. Based on the low level of genetic diversity, the existence of a long-term population decline or a past recent population expansion following a population bottleneck could be proposed in S. guggenheim. This demographic differentiation suggests a degree of vulnerability to overexploitation in this endemic and endangered south-west Atlantic Ocean shark, given its longevity and low reproductive potential.

Molecular and Chromosomal Markers for Evolutionary Considerations in Torpediniformes (Chondrichthyes, Batoidea)

Due to their basal position in the vertebrate phylogenetic tree, the study on elasmobranch genetics and cytogenetics can provide remarkable information on the mechanisms underlying the evolution of all vertebrates. In recent years, different molecular approaches have been used to study the relationships between the different taxonomic groups of cartilaginous fish, among them are the physical mapping of specific nucleotide sequences on chromosomes. However, these are controversial, particularly in Torpediniformes in which the species have different karyological parameters. The purpose of this paper is to gather the molecular markers so far present in literature that were used to reconstruct the phylogenetic position of Torpediniformes with respect to the other Batoidea and to discriminate between the various chromosome pairs in the endemic species in the Mediterranean Sea, Torpedo torpedo, T. marmorata and T. nobiliana. The 5S and 18S ribosomal DNA, the HpaI and Alu SINE, the telomeric (TTAGGG)n and the spermatogenesis-related SPATA 16, SPATA 18, and UTY sequences were particularly useful. These last genomic segments were also able to differentiate between the male and the female karyotypes. Moreover, the torpedoes showed a particular genomic organization, especially Torpedo torpedo, in which large quantities of highly repeated DNA and a characteristic distribution of heterochromatin, which is never centromeric, were observed.

Evolutionary relations of Hexanchiformes deep-sea sharks elucidated by whole mitochondrial genome sequences

Hexanchiformes is regarded as a monophyletic taxon, but the morphological and genetic relationships between the five extant species within the order are still uncertain. In this study, we determined the whole mitochondrial DNA (mtDNA) sequences of seven sharks including representatives of the five Hexanchiformes, one squaliform, and one carcharhiniform and inferred the phylogenetic relationships among those species and 12 other Chondrichthyes (cartilaginous fishes) species for which the complete mitogenome is available. The monophyly of Hexanchiformes and its close relation with all other Squaliformes sharks were strongly supported by likelihood and Bayesian phylogenetic analysis of 13,749 aligned nucleotides of 13 protein coding genes and two rRNA genes that were derived from the whole mDNA sequences of the 19 species. The phylogeny suggested that Hexanchiformes is in the superorder Squalomorphi, Chlamydoselachus anguineus (frilled shark) is the sister species to all other Hexanchiformes, and the relations within Hexanchiformes are well resolved as Chlamydoselachus, (Notorynchus, (Heptranchias, (Hexanchus griseus, H. nakamurai))). Based on our phylogeny, we discussed evolutionary scenarios of the jaw suspension mechanism and gill slit numbers that are significant features in the sharks.

Revealing less derived nature of cartilaginous fish genomes with their evolutionary time scale inferred with nuclear genes

Cartilaginous fishes, divided into Holocephali (chimaeras) and Elasmoblanchii (sharks, rays and skates), occupy a key phylogenetic position among extant vertebrates in reconstructing their evolutionary processes. Their accurate evolutionary time scale is indispensable for better understanding of the relationship between phenotypic and molecular evolution of cartilaginous fishes. However, our current knowledge on the time scale of cartilaginous fish evolution largely relies on estimates using mitochondrial DNA sequences. In this study, making the best use of the still partial, but large-scale sequencing data of cartilaginous fish species, we estimate the divergence times between the major cartilaginous fish lineages employing nuclear genes. By rigorous orthology assessment based on available genomic and transcriptomic sequence resources for cartilaginous fishes, we selected 20 protein-coding genes in the nuclear genome, spanning 2973 amino acid residues. Our analysis based on the Bayesian inference resulted in the mean divergence time of 421 Ma, the late Silurian, for the Holocephali-Elasmobranchii split, and 306 Ma, the late Carboniferous, for the split between sharks and rays/skates. By applying these results and other documented divergence times, we measured the relative evolutionary rate of the Hox A cluster sequences in the cartilaginous fish lineages, which resulted in a lower substitution rate with a factor of at least 2.4 in comparison to tetrapod lineages. The obtained time scale enables mapping phenotypic and molecular changes in a quantitative framework. It is of great interest to corroborate the less derived nature of cartilaginous fish at the molecular level as a genome-wide phenomenon.

Phylogenetic analysis based on 28S rRNA of Babesia spp. in ruminants in China

Molecular phylogenetic analyses are mainly based on the small ribosomal RNA subunit (18S rRNA), internal transcribed spacer regions, and other molecular markers. We compared the phylogenetic relationships of Babesia spp. using large subunit ribosomal RNA, i.e., 28S rRNA, and the united 28S + 18S rRNA sequence fragments from 11 isolates of Babesia spp. collected in China. Due to sequence length and variability, the 28S rRNA gene contained more information than the 18S rRNA gene and could be used to elucidate the phlyogenetic relationships of B. motasi, B. major, and B. bovis. Thus, 28S rRNA is another candidate marker that can be used for the phylogenetic analysis of Babesia spp. However, the united fragment (28S + 18S) analysis provided better supported phylogenetic relationships than single genes for Babesia spp. in China.

A DNA barcode for Piroplasmea

Due to the difficulty in morphological identification the development of reliable molecular tools for species distinction is a priority for piroplasma. Previous studies based on 18S rRNA and other gene sequences provided a backbone for the phylogeny of piroplasma. However, it is difficult to discriminate species in a comprehensive sample. Here, the abilities of eight DNA regions including 18S rRNA, 28S rRNA, internal transcribed spacer (ITS) regions and COI genes, have been compared as candidates of DNA barcodes for piroplasma. In total, 484 sequences of piroplasma were collected from this study and GenBank. The eight proposed DNA regions were evaluated according to the criterion of Consortium for the Barcode of Life (CBOL). From this evaluation, ITS2 had 100% PCR amplification efficiency, an ideal sequence length, the largest gap between the intra- and inter-specific divergence, 98% identification efficiency at the genus level, and 92% at the species level. Thus, we propose that ITS2 is the most ideal DNA barcode based on the current database for piroplasma.

An analytical approach for estimating fossil record and diversification events in sharks, skates and rays

Background

Modern selachians and their supposed sister group (hybodont sharks) have a long and successful evolutionary history. Yet, although selachian remains are considered relatively common in the fossil record in comparison with other marine vertebrates, little is known about the quality of their fossil record. Similarly, only a few works based on specific time intervals have attempted to identify major events that marked the evolutionary history of this group.

Methodology/Principal Findings

Phylogenetic hypotheses concerning modern selachians’ interrelationships are numerous but differ significantly and no consensus has been found. The aim of the present study is to take advantage of the range of recent phylogenetic hypotheses in order to assess the fit of the selachian fossil record to phylogenies, according to two different branching methods. Compilation of these data allowed the inference of an estimated range of diversity through time and evolutionary events that marked this group over the past 300 Ma are identified. Results indicate that with the exception of high taxonomic ranks (orders), the selachian fossil record is by far imperfect, particularly for generic and post-Triassic data. Timing and amplitude of the various identified events that marked the selachian evolutionary history are discussed.

Conclusion/Significance

Some identified diversity events were mentioned in previous works using alternative methods (Early Jurassic, mid-Cretaceous, K/T boundary and late Paleogene diversity drops), thus reinforcing the efficiency of the methodology presented here in inferring evolutionary events. Other events (Permian/Triassic, Early and Late Cretaceous diversifications; Triassic/Jurassic extinction) are newly identified. Relationships between these events and paleoenvironmental characteristics and other groups’ evolutionary history are proposed.

Identification of rays through DNA barcoding: an application for ecologists

DNA barcoding potentially offers scientists who are not expert taxonomists a powerful tool to support the accuracy of field studies involving taxa that are diverse and difficult to identify. The taxonomy of rays has received reasonable attention in Australia, although the fauna in remote locations such as Ningaloo Reef, Western Australia is poorly studied and the identification of some species in the field is problematic. Here, we report an application of DNA-barcoding to the identification of 16 species (from 10 genera) of tropical rays as part of an ecological study. Analysis of the dataset combined across all samples grouped sequences into clearly defined operational taxonomic units, with two conspicuous exceptions: the Neotrygon kuhlii species complex and the Aetobatus species complex. In the field, the group that presented the most difficulties for identification was the spotted whiptail rays, referred to as the ‘uarnak’ complex. Two sets of problems limited the successful application of DNA barcoding: (1) the presence of cryptic species, species complexes with unresolved taxonomic status and intra-specific geographical variation, and (2) insufficient numbers of entries in online databases that have been verified taxonomically, and the presence of lodged sequences in databases with inconsistent names. Nevertheless, we demonstrate the potential of the DNA barcoding approach to confirm field identifications and to highlight species complexes where taxonomic uncertainty might confound ecological data.

What is an 'elasmobranch'? The impact of palaeontology in understanding elasmobranch phylogeny and evolution

The Subclass Elasmobranchii is widely considered nowadays to be the sister group of the Subclass Holocephali, although chimaeroid fishes were originally classified as elasmobranchs along with modern sharks and rays. While this modern systematic treatment provides an accurate reflection of the phylogenetic relationships among extant taxa, the classification of many extinct non-holocephalan shark-like chondrichthyans as elasmobranchs is challenged. A revised, apomorphy-based definition of elasmobranchs is presented in which they are considered the equivalent of neoselachians, i.e. a monophyletic group of modern sharks and rays which not only excludes all stem and crown holocephalans, but also many Palaeozoic shark-like chondrichthyans and even close extinct relatives of neoselachians such as hybodonts. The fossil record of elasmobranchs (i.e. neoselachians) is reviewed, focusing not only on their earliest records but also on their subsequent distribution patterns through time. The value and limitations of the fossil record in answering questions about elasmobranch phylogeny are discussed. Extinction is seen as a major factor in shaping early elasmobranch history, especially during the Triassic. Extinctions may also have helped shape modern lamniform diversity, despite uncertainties surrounding the phylogenetic affinities of supposedly extinct clades such as cretoxyrhinids, anacoracids and odontids. Apart from these examples, and the supposed Cretaceous extinction of 'sclerorhynchids', elasmobranch evolution since the Jurassic has mostly involved increased diversification (especially during the Cretaceous). The biogeographical distribution of early elasmobranchs may be obscured by sampling bias, but the earliest records of numerous groups are located within the Tethyan realm. The break-up of Gondwana, and particularly the opening of the South Atlantic Ocean (together with the development of epicontinental seaways across Brazil and Africa during the Cretaceous), provided repeated opportunities for dispersal from both eastern (European) and western (Caribbean) Tethys into newly formed ocean basins.

A review of the application of molecular genetics for fisheries management and conservation of sharks and rays

Since the first investigation 25 years ago, the application of genetic tools to address ecological and evolutionary questions in elasmobranch studies has greatly expanded. Major developments in genetic theory as well as in the availability, cost effectiveness and resolution of genetic markers were instrumental for particularly rapid progress over the last 10 years. Genetic studies of elasmobranchs are of direct importance and have application to fisheries management and conservation issues such as the definition of management units and identification of species from fins. In the future, increased application of the most recent and emerging technologies will enable accelerated genetic data production and the development of new markers at reduced costs, paving the way for a paradigm shift from gene to genome-scale research, and more focus on adaptive rather than just neutral variation. Current literature is reviewed in six fields of elasmobranch molecular genetics relevant to fisheries and conservation management (species identification, phylogeography, philopatry, genetic effective population size, molecular evolutionary rate and emerging methods). Where possible, examples from the Indo-Pacific region, which has been underrepresented in previous reviews, are emphasized within a global perspective.

Phylogenetics of Chondrichthyes and the problem of rooting phylogenies with distant outgroups

Erroneous estimates of ingroup relationships can be caused by attributes in the outgroup chosen to root the tree. Phylogenetic analyses of DNA sequences frequently yield incorrect estimates of ingroup relationships when the outgroup used to "root" the tree is highly divergent from the ingroup. This is especially the case when the outgroup has a different base composition than the ingroup. Unfortunately, in many instances, alternative less divergent outgroups are not available. In such cases, investigators must either target genes with attributes that minimize the problem (slowly evolving genes with stationary base compositions--which are often not ideal for estimating relationships among the more closely related ingroup taxa) or use inference models that are explicitly tailored to deal with an attenuated historical signal with a superimposed non-stationary base composition. In this paper we explore the problem both empirically and through simulation. For the empirical component we looked at the phylogenetic relationships among elasmobranch fishes (sharks and rays), a group whose closest living outgroup, the holocephalan Ghost fishes, are separated from the elasmobranchs by more than 100 million years of evolution. We compiled a data set for analysis comprising 10 single-copy nuclear protein-coding genes (12,096 bp) for representatives of the major lineages within elasmobranchs and holocephalans. For the simulation, we used an evolutionary model on a fixed tree topology to generate DNA sequence data sets which varied both in their distance to the outgroup, and in their base compositional difference between ingroup and outgroup. Results from both the empirical data set and the simulation, support the idea that deviation from base compositional stationarity, in conjunction with distance from the root can act in concert to compromise accuracy of estimated relationships within the ingroup. We tested several approaches to mitigate such problems. We found, that excluding genes with overall faster rates and heterogeneous base compositions, while the least sophisticated of the methods evaluated, seemed to be the most effective.

First taxonomic description of multivalvulidan myxosporean parasites from elasmobranchs: Kudoa hemiscylli n.sp. and Kudoa carcharhini n.sp. (Myxosporea: Multivalvulidae)

Myxosporean parasites are significant parasites of fishes not only for their apparent high diversity but also for their potential impact on fish health and/or marketability. Regardless, our knowledge of most myxosporeans, especially those found in elasmobranch hosts, is superficial. A study of multivalvulidan diversity in a range of elasmobranchs from Queensland, Western Australia and the Northern Territory (Australia) was conducted to address this knowledge gap. Specimens were collected from a total of 3 orders, 9 families and 31 species of elasmobranchs. Myxosporean infections referable to the genus Kudoa were discovered in host muscle and characterized morphologically and genetically. Both small subunit (SSU) and large subunit (LSU) rDNA sequences were used in molecular phylogenetic analyses. Kudoa spp. infected 27 of the 31 species of elasmobranchs examined, representing new records of this parasite genus in 26, of the 27, host species. Kudoids were observed in all 3 orders, and 7 out of the 9 families of elasmobranchs investigated. This paper reports the first 2 multivalvulidan species to be formally described from elasmobranchs, Kudoa hemiscylli n.sp. characterized from Hemiscyllium ocellatum (and 8 other host species) and Kudoa carcharhini n. sp. characterized from Carcharhinus cautus (and 2 other host species). Phylogenetic analyses revealed that kudoids from elasmobranchs form a separate lineage to those of teleosts, but are anchored within the overall kudoid clade.

Evolutionary origin and phylogeny of the modern holocephalans (Chondrichthyes: Chimaeriformes): a mitogenomic perspective

With our increasing ability for generating whole-genome sequences, comparative analysis of whole genomes has become a powerful tool for understanding the structure, function, and evolutionary history of human and other vertebrate genomes. By virtue of their position basal to bony vertebrates, cartilaginous fishes (class Chondrichthyes) are a valuable outgroup in comparative studies of vertebrates. Recently, a holocephalan cartilaginous fish, the elephant shark, Callorhinchus milii (Subclass Holocephali: Order Chimaeriformes), has been proposed as a model genome, and low-coverage sequence of its genome has been generated. Despite such an increasing interest, the evolutionary history of the modern holocephalans-a previously successful and diverse group but represented by only 39 extant species-and their relationship with elasmobranchs and other jawed vertebrates has been poorly documented largely owing to a lack of well-preserved fossil materials after the end-Permian about 250 Ma. In this study, we assembled the whole mitogenome sequences for eight representatives from all the three families of the modern holocephalans and investigated their phylogenetic relationships and evolutionary history. Unambiguously aligned sequences from these holocephalans together with 17 other vertebrates (9,409 nt positions excluding entire third codon positions) were subjected to partitioned maximum likelihood analysis. The resulting tree strongly supported a single origin of the modern holocephalans and their sister-group relationship with elasmobranchs. The mitogenomic tree recovered the most basal callorhinchids within the chimaeriforms, which is sister to a clade comprising the remaining two families (rhinochimaerids and chimaerids). The timetree derived from a relaxed molecular clock Bayesian method suggests that the holocephalans originated in the Silurian about 420 Ma, having survived from the end-Permian (250 Ma) mass extinction and undergoing familial diversifications during the late Jurassic to early Cretaceous (170-120 Ma). This postulated evolutionary scenario agrees well with that based on the paleontological observations.

The evolution of gnathostome development: Insight from chondrichthyan embryology

Chondrichthyans (cartilaginous fishes) represent one of the two lineages of gnathostomes, the other being the osteicthyans (bony fishes). Classical studies on chondrichthyan embryology have strongly impacted our views of vertebrate body plan evolution, while recent studies highlight oviparous chondrichthyans as emerging vertebrate model systems that are amenable to experimental embryological manipulation. Here, we review three particular areas of interest in the field of chondrichthyan developmental biology-gastrulation, neural development, and appendage patterning-and we discuss recent findings within a broader chondrichthyan-osteichthyan comparative framework. In some cases, comparative studies of chondrichthyan and osteichthyan development reveal conserved patterns of gene expression in common developmental contexts. Studies of chondrichthyan gastrulation reveal conserved patterns of developmental gene expression, despite highly divergent modes of mesendoderm internalization, while molecular characterization of chondrichthyan neurogenic placodes indicates a conservation of placode transcription factor expression across gnathostome phylogeny. In other cases, comparative studies of chondrichthyan and osteichthyan development yield evidence of shared patterning mechanisms functioning in different developmental contexts. This is exemplified by studies on the development of chondrichthyan appendages-paired fins, median fins, and gill rays. These have demonstrated that a retinoic acid-responsive Shh-expressing signaling center functions to pattern the endoskeleton of gnathostome paired fins and chondrichthyan gill rays, while expression patterns of Tbx18 and HoxD family members are shared by gnathostome paired fins and chondrichthyan median fins. These findings fuel novel hypotheses of developmental genetic homology, and demonstrate how comparative studies of gnathostome development can provide insight into the evolutionary processes that underlie morphological diversity.

Molecular systematics and global phylogeography of angel sharks (genus Squatina)

Angel sharks of the genus Squatina represent a group comprising 22 extant benthic species inhabiting continental shelves and upper slopes. In the present study, a comprehensive phylogenetic reconstruction of 17 Squatina species based on two mitochondrial markers (COI and 16S rRNA) is provided. The phylogenetic reconstructions are used to test biogeographic patterns. In addition, a molecular clock analysis is conducted to estimate divergence times of the emerged clades. All analyses show Squatina to be monophyletic. Four geographic clades are recognized, of which the Europe-North Africa-Asia clade is probably a result of the Tethys Sea closure. A second sister group relationship emerged in the analyses, including S. californica (eastern North Pacific) and S. dumeril (western North Atlantic), probably related to the rise of the Panamanian isthmus. The molecular clock analysis show that both lineage divergences coincide with the estimated time of these two geological events.