• cryptic species
• integrative taxonomy
• Paraonidae
• phylogeny

Although a number of morphological studies gave new insights into the evolution of annelids, the contribution of molecular surveys to clarify the relationships at low taxonomic levels is still scarce. Paraonidae is one of the most interesting family of polychaetes from this point of view, because it gave rise to an extremely wide adaptive radiation on soft bottoms and currently shows an extremely high species diversity. The relationships among the genera of Paraonidae, as well as those among the subgenera of Aricidea, are still unclear, and attempts of investigating this issue with phylogenetic inference based on morphological features gave indecisive results, because of the simple anatomy of these worms and the scarcity of sound morphological characters. Moreover, the phylogenetic relevance of morphological features considered informative for Paraonidae has not been proved yet. This thesis is aimed to give a deep insight into the diversity and evolution of Paraonidae, employing a combined molecular and morphological approach.
The identity of the Mediterranean material traditionally referred to Cirrophorus furcatus (Hartman, 1957) is critically discussed on the basis of morphological and molecular data. The Mediterranean material historically referred to this taxon can be assigned to two undescribed species, Cirrophorus sp. A and Cirrophorus sp. B. The former species, commonly occurring in brackish-water and other organically enriched environments, is characterised by high number of branchiae; whereas Cirrophorus sp. B, probably restricted to marine environments, is characterised by low number of branchiae. Moreover, a preliminary phylogenetic analysis allowed to reject the synonymy between Cirrophorus and Paradoneis, as molecular data identify two monophyletic highly supported clades. This outcome represents a first clue that evolutionary history of Paraonidae is less linear than previously suggested.
Aricidea assimilis Tebble, 1959, a common Mediterranean Paraonidae, was employed as model species to test the effect of environmental breaks and biogeographical barriers on genetic diversity in this family. Molecular data showed a high degree of genetic divergence between deep- and shallow-water lineages. A less pronounced, but statistically significant, divergence was detected between brackish-water and marine sub-lineages within the shallow-water lineage. Moreover, the brackish-water sub-lineage was morphologically differentiated from the remaining individuals of A. assimilis examined. The levels of molecular divergence between the deep- and the shallow-water lineages are consistent with the hypothesis of cryptic species, whereas the divergence identified between brackish-water and marine individuals can be considered representative of incipient speciation. Interestingly, geographical genetic structuring was not detected in any of the examined lineages, suggesting that Paraonidae have wide dispersal larval phases, in contrast to the widespread belief on the predominance of direct development in this family.
A morpho-molecular approach was employed to test the alleged cosmopolitanism of Aricidea catherinae Laubier, 1967. The examination of individuals from the western Pacific Ocean, western and eastern Atlantic Ocean and the Mediterranean Sea, identified as A. catherinae, led to the conclusion that they belong to six different species, four of which are undescribed. Individuals identified as A. catherinae on the basis of chaetal shape belonged to three highly supported clades that were not directly related, suggesting that neuropodial modified chaetae, which were considered typical of A. catherinae, are actually widespread within the genus Aricidea and might represent a symplesiomorphic character for this genus. Conversely, several overlooked morphological features, such as fine details of the chaetae and shape of the antenna, have been re-evaluated as taxonomically informative. This study on A. catherinae highlighted the occurrence of several undescribed species within an allegedly cosmopolitan nominal taxon. Similar cases have been reported in a number of polychaete families and are expected to impinge on species checklists and ultimately on environmental assessment and monitoring.
Lastly, a comprehensive phylogeny of all available Paraonidae genera, based on 60 individuals belonging to 34 nominal species, was carried out. This work, carried out by means of two mitochondrial (COI and 16S rDNA) and one nuclear (18S rDNA) markers, showed an evolutionary history more complex than previously suggested. Paraonidae analysed in the present work were composed by five highly supported clades. Species of the genera Cirrophorus and Paradoneis were included in two independent clades. The genus Aricidea was monophyletic with the inclusion of Paraonis and the exclusion of four morphologically homogeneous nominal species that represent an undescribed genus, here denominated New Genus A (NGA). NGA is morphologically close to the monophyletic genus Levinsenia as regards the shape of prostomium and of modified neurochaetae, and molecular analyses confirmed this close relatedness. In addition, this phylogenetic reconstruction shed light on the evolution of some morphological features of Paraonidae. Reasonably, lyrate modified notochaetae represent the ancestral trait that later underwent modifications: In one lineage lyrate chaetae became thicker and harpoon-like, whereas in the other lineage, including Aricidea, Levinsenia and New Genus A, neuropodial modified chaetae were completely lost. On the other hand, modified neurochaetae were sporadically present in the earliest branching lineages, and became firmly stabilised only in Aricidea, Levinsenia and NGA, reaching the greatest variability in Aricidea. The adaptation to bathyal environments seems to have occurred several times along the evolutionary history of this family, starting from shallow-water ancestors. Based on present data, therefore, the ancestral Paraonidae should have been a shallow-water polychaete with three pre-branchial chaetigers and lyrate notochaetae, with or without modified neurochaetae, with or without prostomial antenna. From a strictly taxonomic perspective the phylogenetic reconstruction highlighted the occurrence of a number of cryptic or pseudocryptic species within nominal taxa.
The study of evolutionary processes in marine environments is of paramount importance to understand the role played by environmental modifications, among which anthropogenic changes and global warming. The first step towards the understanding of such processes is however a correct assessment of biological diversity within organism groups. Taxonomic expertise has been neglected in the last decades, but is indeed crucial both for environmental assessment, and for validation of molecular surveys that are expected to partially replace traditional environmental monitoring techniques. This thesis confirmed the key role of integrative taxonomy as a synergistic approach towards the understanding of evolutionary patterns and processes.