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.

The ongoing decline in abundance and diversity of shark stocks, primarily due to uncontrolled fishery exploitation, is a worldwide problem. An additional problem for the development of conservation and management programmes is the identification of species diversity within a given area, given the morphological similarities among shark species, and the typical disembarkation of processed carcasses which are almost impossible to differentiate. The main aim of the present study was to identify those shark species being exploited off northern Brazil, by using the 12S-16S molecular marker. For this, DNA sequences were obtained from 122 specimens collected on the docks and the fish market in Bragança, in the Brazilian state of Pará. We identified at least 11 species. Three-quarters of the specimens collected were either Carcharhinus porosus or Rhizoprionodon sp, while a notable absence was the daggernose shark, Isogomphodon oxyrhyncus, previously one of the most common species in local catches. The study emphasises the value of molecular techniques for the identification of cryptic shark species, and the potential of the 12S-16S marker as a tool for phylogenetic inferences in a study of elasmobranchs.

Molecular phylogenetic studies are very scarce for the Mugilidae family; the present analysis using DNA sequences of the mitochondrial 16S rRNA and cytochrome b genes is the first study involving Brazilian mugilids. The results corroborate the monophyly of Mugil and are elucidative for the taxonomy of Brazilian mugilids. Mugil curema is clearly divided into two genetically distinct taxa, M. curema type I being closer related to Mugil hospes and the true M. curema (type II) grouping significantly with M. incilis. The results also suggest that Mugil liza and Mugil platanus should be treated as a single species or even populations of Mugil cephalus.

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.

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