Population genetic, phylogenetic and sex-related gene expression analyses in two "Palaemon" species

Abstract

The rockpool shrimp Palaemon elegans and the common littoral shrimp P. serratus are two ecologically important crustacean species on European coastlines. Palaemon serratus is also an economically relevant resource, since it is considered a prized delicacy in European markets. This PhD thesis aims to contribute to the understanding of the population and reproductive biology of P. elegans and P. serratus by investigating the underlying genetics. Firstly, a phylogeographic analysis was carried out in P. elegans using twenty-one newly developed microsatellite loci. A Mediterranean sympatric cryptic species was revealed, while genetic differentiation was detected in P. elegans sensu stricto across the Atlantic-Mediterranean transition area, with the Almería-Orán Front as biogeographical barrier. Secondly, seven Palaemon mitochondrial genomes, including those of P. elegans and P. serratus, were described and used to conduct phylogenetic analyses. The cryptic species within P. elegans was confirmed, and the Messinian Salinity Crisis was disclosed as its origin. Furthermore, we proposed that the Atlantic and Mediterranean lineages of P. serratus could actually be two separated species. Finally, a gonadal reference transcriptome of P. serratus was de novo assembled and annotated. The first findings on sex-related genes were reported, providing new insights into the sexual development of this commercial species.