Stochastic modeling of bacterial protein domains distribution to predict horizontal gene transfer

In questo elaborato, abbiamo tentato di modellizzare i processi che regolano la presenza dei domini proteici. I domini proteici studiati in questa tesi sono stati ottenuti dai genomi batterici disponibili nei data base pubblici (principalmente dal National Centre for Biotechnology Information: NCBI) tramite una procedura di simulazione computazionale. Ci siamo concentrati su organismi batterici in quanto in essi la presenza di geni trasmessi orizzontalmente, ossia che parte del materiale genetico non provenga dai genitori, e assodato che sia presente in una maggiore percentuale rispetto agli organismi più evoluti. Il modello usato si basa sui processi stocastici di nascita e morte, con l'aggiunta di un parametro di migrazione, usato anche nella descrizione dell'abbondanza relativa delle specie in ambito delle biodiversità ecologiche. Le relazioni tra i parametri, calcolati come migliori stime di una distribuzione binomiale negativa rinormalizzata e adattata agli istogrammi sperimentali, ci induce ad ipotizzare che le famiglie batteriche caratterizzate da un basso valore numerico del parametro di immigrazione abbiano contrastato questo deficit con un elevato valore del tasso di nascita. Al contrario, ipotizziamo che le famiglie con un tasso di nascita relativamente basso si siano adattate, e in conseguenza, mostrano un elevato valore del parametro di migrazione. Inoltre riteniamo che il parametro di migrazione sia direttamente proporzionale alla quantità di trasferimento genico orizzontale effettuato dalla famiglia batterica.

Ecological distribution of semi-demersal fishes in space and time on the shelf of Antalya Gulf

In this study we provide a baseline data on semidemersal fish assemblages and biology in a heterogeneous and yet less studied portion of the shelf of Antalya Gulf. The distribution of fish abundance in three transects subjected to different fisheries regulations (fishery vs non fishery areas), and including depths of 10, 25, 75, 125, 200 m, was studied between May 2014 and February 2015 in representative months of winter, spring, summer and autumn seasons. A total of 76 fish species belonging to 40 families was collected and semidemersal species distribution was analyzed in comparison with the whole community. Spatial distribution of fish was driven mainly by depth and two main assemblages were observed: shallow waters (10-25; 75 m) and deep waters (125-200 m). Significant differences among transects were found for the whole community but not for the semidemersal species. Analysis showed that this was due to a strong relation of these species with local environmental characteristics rather than to a different fishing pressure over transects. Firstly all species distribute according to the bathymetrical gradient and secondly to the bottom type structure. Semidemersal species were then found more related to zooplankton and suspended matter availability. The main morphological characteristics, sex and size distribution of the target semidemersal species Spicara smaris (Linnaeus, 1758), Saurida undosquamis (Richardson, 1848), Pagellus acarne (Risso, 1827) were also investigated.

Polychaete fauna of the Northwest Portuguese Coastal Shelf: ecology, diversity and distribution

Polychaetes are one of the larger groups of macroinvertebrates with more than 9000 species recognised, distributed worldwide. Thanks to the broad ecological adaptability and high abundaces, this taxon plays a leading role and is considered an important component of all benthic assemblages. Our knowledge about the West Iberian Coast polychaete fauna are scarce, and the only studies are recent. In this sense, the aim of this work was to investigate the composition and the spatial distribution of the polychaete fauna along the NW Portuguese Coastal Shelf, focusing on their relationship to environmental factors (depth, grain size, longitude and latitude) and to add new data to the existing biological dataset. A total of 39 sites were analysed, collected in an area of about 5665 km², between 20 and 150 m depth, distributed in a way to cover the overall grain size gradient. A total of 9352 specimens belonging to 41 families were found, and the analysis based on the abundance of polychaete species revealed five affinity groups: (a) nearshore medium sand characterised by Pisione parapari and Hesionura elongata; (b) very coarse sand that showed the highest abundance of Syllidae and was characterised by Protodorvillea kefersteini and Syllis garciai; (c) fine sand dominated by Spiophanes bombyx and Glycera tridactyla; (d) very fine sand with Nepthys assimilis and Amage sp. and the highest abundance of Paraonidae; (d) mud characterised by Labioleanira yhleni and Ampharete finmarchica. The combination of the environmental variables and the biological data, done with BIOENV routine, demonstrated that depth, grain size and fine contents were the best related with the biological data (rho=0.598). In general, the results agree with the composition and the spatial distribution of the polychaete fauna in other parts of the world; further polychaete assemblages related to mud sediments were firstly recorded in the Northwestern Portuguese Coastal Shelf.