Molecular genetics of aliens in Maltese waters

Abstract

The Mediterranean Sea is a hotspot of marine biodiversity, characterised by endemism and host to emblematic species of concern for conservation. Yet its habitats and ecosystems face many threats of anthropogenic origin, among the most prominent of which are biological invasions. Their initial introduction facilitated primarily by the opening of the Suez Canal, fouling and the transport of ballast water along shipping routes, invasive alien species have on several occasions caused rapid population declines, range shifts, and even local extirpations. Such ecological declines have in turn incurred the states that border the Mediterranean Sea costs amounting to billions of euros, ultimately prompting the enactment of Union-level regulations that demand the early detection and rapid eradication of the alien species invading the basin. The capacity to identify alien species is fundamental to their effective management. Their monitoring necessitates the use of diagnostic tools that are accurate, readily deployable, cost-effective, and applicable across a range of taxa. Traditional approaches to identification that are reliant on morphological characteristics fall short of these criteria, prompting in turn investigations into novel molecular approaches. This provided, the scope of the present project was to investigate the applicability of the cytochrome c oxidase subunit I (COI) gene in identifying newcomers to Maltese coastal waters and to contrast the genetic data it yields with morphological lines of evidence as part of an integrative approach towards correct species identification. Specimens from diverse metazoan taxa suspected to be of alien origin were collected and their morphologies documented. Tissue samples were excised from each specimen and treated with proteinase K for DNA extraction. Segments of the COI gene were then amplified, sequenced, and compared with the genetic data available in the international repositories of GenBank and BOLD. Genetic species identifications were thus derived and complemented with morphological species identifications. Phylogenetic trees of maximum likelihood were also constructed. The molecular approach described above allowed for the species identification of a total of 57 specimens. This enabled in turn the reliable distinction of alien specimens from native specimens. Morphological identifications corroborating the genetic identifications were possible for 50 specimens. Moreover, the single specimen of Siganus rivulatus presented here constitutes the first record of the species for the Maltese Islands. 12 of the haplotypes sequenced in the process of completing this project constitute newly discovered genetic variants for 7 species. The results of the present project emphasise the need for a molecular approach to species identification, especially in scenarios where: specimen morphologies are largely lost or deteriorated; morphological keys are not sufficiently informative; and specimen morphologies are cryptic or at least highly similar. Ultimately, the integration of genetic and morphological lines of evidence throughout this project produced a more robust approach that consistently guided the research undertaken towards accurate specimen identification. This approach’s application in regimes tasked with detecting, managing, and preventing marine invasions is thus recommended.