Differential Gene Expression of Dorsal Pictorial Ornaments and Pigmentation in Skates (Rajidae, Chondrichthyes)

Approximately twenty years have passed since the beginning of concentrated investigations on the evolution and ecology of skates. The evidence generated thus far suggested that this monophyletic group have experienced multiple, parallel adaptive radiations at a regional scale. This background represented the guiding light of the work described in this thesis, where two main themes were developed. The first one focused on the investigation of Raja miraletus L. species complex through the analysis of genetic variation derived from both mtDNA and nuDNA. The results presented herein assessed the presence of a restricted gene flow and different degree of divergence between the South African and Mediterranean samples. Despite the high species diversity characterising the Family, most Rajidae show a stable gross morphology and peculiar dorsal pigmentation patterns, which may have been implicated in cryptic speciation. Nonetheless, the adaptive value and the genetic basis of these traits remain poorly investigated. To fill this gap, this thesis also describes the application of RNA-sequencing technology on recently diverged skate species with sibling and sister phylogenetic relationships. Therefore, the second goal of this research consisted in investigating the molecular basis of pigmentation in five non-model species. To this end, the transcriptome profiling of different skin tissues was performed using the Illumina platform, whereas longer sequencing data were obtained from R. miraletus multiple organs using the Ion Torrent technology. After the assembly of a reference transcriptome and the mapping of Illumina reads, the Differential Gene Expression between skin tissues across species was performed, revealing the expression of transcripts mainly related to metabolic process and catalytic activity in which pigmentary genes appeared involved. This work could be considered the basis for future studies aiming to disentangle how pigmentary traits evolved in skates and other chondrichtyans.