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.
Part of the book: Chondrichthyes