A Review of the Mitogenomic Phylogeny of the Chondrichthyes

The phylogenetic analysis of the Chondrichthyes has been the subject of intense debate over the past two decades. The principal relationships within the group based on the analysis of morphological traits are inconsistent with the available molecular topologies, and the phylogeny of these animals is highly controversial, at all levels, ranging from superorders to families and even the genera within families. With the recent development of new generation sequencing (NGS), many phylogenies are now being inferred based on the complete genome of the species. In 2015 and 2016 alone, around 21 new elasmobranch genomes were made available in GenBank. In this context, the principal objective of the present study was to infer the phylogeny of the sharks and rays based on the complete mitochondrial genomes available in the literature. A total of 73 mitogenomes of chondrichthyan species were analyzed. The phylogenetic trees generated rejected the “Hypnosqualea” hypothesis and confirmed the monophyly of the Neoselachii and Batoidea as sister groups of the sharks. These mitogenomic analyses provided ampler and more complete insights into the relationships between the sharks and rays, in particular, the topologies obtained by the analyses revealed a number of incongruities in certain groups of sharks and rays, and the interrelationships between them

Commercialization of a critically endangered species (largetooth sawfish, Pristis perotteti) in fish markets of northern Brazil: Authenticity by DNA analysis

AbstractPristis perotteti, the largetooth sawfish, is one of most endangered elasmobranchs because of fisheries and habitat degradation. Its commercialization in Brazil is prohibited, but fresh or salted fillets of this fish can be found in markets, labeled as “sharks”. In this study we performed genetic analyses on “shark” samples from two important fishery-trading ports in northern Brazil (Vigia and Bragança). Based on partial DNA sequences of the mitochondrial 16S and Cyt b genes, 24 (55%) out of 44 samples were unequivocally identified as P. perotteti while the others comprised eight species of the families Carcharhinidae and Ginglymostomatidae. These results show that fishing surveillance and monitoring have not been effective to prohibit the commercialization of this highly endangered species

Molecular Phylogeny of the Genus Lolliguncula Steenstrup, 1881 Based on Nuclear and Mitochondrial DNA Sequences Indicates Genetic Isolation of Populations from North and South Atlantic, and the Possible Presence of Further Cryptic Species

Squid of the genus Lolliguncula Steenstrup, 1881 are small bodied, coastal species capable of tolerating low salinity. Lolliguncula sp. are found exclusively in the New World, although only one of the four recognized species (Lolliguncula brevis) occurs in the Atlantic Ocean. Preliminary morphological analyses suggest that Lolliguncula brevis populations in the North and South Atlantic may represent distinct species. The principal objective of the present study was to verify the phylogenetic relationships within the genus and test for the presence of possible cryptic species. Both gene and species tree topologies indicated that Lolliguncula brevis specimens from the North and South Atlantic represent distinct phylogenetic clades. In contrast with previous studies, L. panamensis was identified as the basal species of the genus. Our results provide important insights into the phylogenetic relationships among the Lolliguncula specimens analyzed, and confirm the genetic separation of Lolliguncula brevis populations of the North and South Atlantic at the level of sister species

DNA-based identification reveals illegal trade of threatened shark species in a global elasmobranch conservation hotspot

Here, we report trading of endangered shark species in a world hotspot for elasmobranch conservation in Brazil. Data on shark fisheries are scarce in Brazil, although the northern and northeastern regions have the highest indices of shark bycatch. Harvest is made primarily with processed carcasses lacking head and fins, which hampers reliable species identification and law enforcement on illegal catches. We used partial sequences of two mitochondrial genes (COI and/or NADH2) to identify 17 shark species from 427 samples being harvested and marketed on the northern coast of Brazil. Nine species (53%) are listed under some extinction threat category according to Brazilian law and international authorities (IUCN - International Union for Conservation of Nature; CITES - Convention on International Trade of Endangered Species of Wild Fauna and Flora). The number increases to 13 (76%) if we also consider the Near Threatened category. Hammerhead sharks are under threat worldwide, and composed 18.7% of samples, with Sphyrna mokarran being the fourth most common species among samples. As illegal trade of threatened shark species is a worldwide conservation problem, molecular identification of processed meat or specimens lacking diagnostic body parts is a highly effective tool for species identification and law enforcement

Chondrichthyes - Multidisciplinary Approach

Chondrichthyes are a group of cartilaginous fish, where we have sharks, rays, and chimeras as members. This group plays an important role in aquatic ecology, as they act as predators throughout the food chain (e.g., sharks). However, many populations of Chondrichthyes are threatened by several factors (increased direct fishing, high mortality rate as accompanying fauna, marine pollution, habitat destruction, etc.). These declines are evident in many parts of the world and have come to the attention of scientists, conservation organizations, the media, and the general public. Fisheries legislation regulating international fisheries markets has been amended to provide greater protection for this group along with other species of fish. However, little is known about these species, which reinforces the importance of studies in order to have a better understanding of the elasmobranch stocks, as well as to identify the influences of the anthropic action of fishing. In response to knowledge on the low sustainability of cartilaginous fish fisheries on a global scale, FAO has developed an international plan of action for the management and conservation of these fish, with the aim of developing and implementing national plans of action to ensure management and conservation of these stocks, having as main recommendation the collection of information about the Chondrichthyes, especially the sharks. Even so, this group is little known in terms of biodiversity, ecology, behavior, and a host of other characteristics relevant to this taxon, which is very worrying. Chondrichthyes - Multidisciplinary Approach attempts to portray to the readers up-to-date information on Chondrichthyes to promote an overview of the current taxon, serving as an indispensable source of access to more accurate and detailed information on shark rays and chimeras

Molecular differentiation of the species of two squid families (Loliginidae and Ommastrephidae) based on a PCR study of the 5S rDNA gene

The present study aimed to demonstrate the effectiveness of the 5s rDNA gene for the identification of commercially-valuable species of cephalopod belonging to the families Loliginidae and Ommastrephidae. Our results demonstrate distinct banding patterns in each of the six species sampled (Loligo surinamensis; Loligo sanpaulensis; Lolliguncula brevis; Sepiotheuthis sepioidea; Ornithoteuthis antillarum; Illex argentinus), as well as diagnostic traits at the genus and probably family levels. The results emphasize the efficiency of the 5s rDNA marker as a low-cost and rapid forensic technique, which not only permits the identification of species, but also differentiation of members of the Loliginidae and Ommastrephidae

New molecular phylogeny of the squids of the family Loliginidae with emphasis on the genus Doryteuthis Naef, 1912:Mitochondrial and nuclear sequences indicate the presence of cryptic species in the southern Atlantic Ocean

The family Loliginidae Lesueur, 1821, is currently considered to include seven genera and approximately 50 species of neritic and coastal squids. These commercially important species occur in tropical and temperate coastal waters around the world. The taxonomy of the family has been revised a number of times in recent years, focusing in particular on genera such as Doryteuthis, Sepioteuthis, Alloteuthis, and Uroteuthis, which are represented by populations in the New World, Oceania, Europe/Africa, and Asia. However, no detailed phylogenetic analysis is available for the loliginids of the southern Atlantic, in particular the genus Doryteuthis. The present molecular study analyzed 81 loliginid taxa from around the world. The partial sequencing of the mitochondrial 16S and Cytochrome Oxidase I genes, and the nuclear rhodopsin gene revealed a number of important patterns, recovering the monophyletic status of the majority of the genera and revealing possible cryptic species in Doryteuthis plei D. pealei, Uroteuthis duvauceli and Sepioteuthis lessonianaPeer reviewe