Molecular phylogeny of the prickly shark, Echinorhinus cookei, based on a nuclear (18S rRNA) and a mitochondrial (cytochrome b) gene

Genetic and Distribution Data of the Bramble Shark Echinorhinus brucus (Bonnaterre, 1788) and the Prickly Shark Echinorhinus cookei Pietschmann, 1928 to Better Reconstruct Their Conservation Status

Elasmobranch species show low resilience in relation to anthropogenic stressors such as fishing efforts, loss of habitats, and climate change. In this sense, the elasmobranch populations appear to be at risk of extinction in many cases. Despite conservation researchers making efforts to implement knowledge, the information on the biology, reproduction, distribution, or genetic structure of some species is still scattered, often caused by the occurrence of species in inaccessible habitats. Echinorhinus brucus is a deep benthic shark evaluated as "Endangered" on which little information is available, particularly about its geographical range and genetic structure, while E. cookei is listed as "Data Deficient". Echinorhinus brucus belongs to the Echinorhinidae family, and its unique congeneric species is E. cookei. The main morphological diagnostic characteristic of both species is the presence of denticles with different shapes and patterns on the derma. In the present paper, mitochondrial COI and NADH2 sequences were retrieved from both E. brucus and E. cookei species, and analyses were conducted by applying different models of phylogenetic inference. Sequences of E. brucus captured in the Indian Ocean (IOS) did not cluster with the Atlantic E. brucus counterparts (AOS) but instead with E. cookei sequences; the different models showed an overlapping tree topology. Concurrently, a review of the historical and recent captures of the two species was carried out. The worldwide distribution of E. brucus excludes the Pacific Ocean area, where E. cookei occurs, and is characterised by presumably current local extinctions in the North Sea and the western Mediterranean Sea. The dataset describes two definite areas of significantly high abundance of E. brucus located in the Atlantic Ocean (Brazil) and the Indian Ocean (India). These areas suggest zones for conservation plans, especially considering the two lineages identified through molecular approaches.

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.

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.

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.

Cloning and characterization of a repetitive DNA detected by HindIII in the genome of Raja montagui (Batoidea, Chondrichthyes)

A repetitive HindIII fragment of DNA from Raja montagui (Rajiformes) was cloned and sequenced for the first time in cartilaginous fishes. This element, which comprises approximately 5% of the whole genome of the spotted ray, is absent in long tandem arrays, being typical of satellite DNA. It appeared constituted by 311 AT-rich bp (61%). The clone was hybridized to the genomic DNA of species with varying phyletic distances, revealing a high degree of conservation.

The isochore organization of the human genome and its evolutionary history--a review

This review will first present some properties (including compositional pattern, correlations between isochores and chromosomal bands, and gene distribution) of the human genome, the most extensively studied among vertebrate genomes. It will then explain how these properties came about during the evolution of the vertebrates.