Isolation By Distance (IBD) signals in the deep-water rose shrimp Parapenaeus longirostris (Lucas, 1846) (Decapoda,Panaeidae) in the Mediterranean Sea

The identification of boundaries of genetic demes is one of the major goals for fishery management, and few Mediterranean commercial species have not been studied from a genetic point of view yet. The deep-water rose shrimp Parapenaeus longirostris (Lucas, 1846) is one of the most important components of commercial landings in Mediterranean, its fishery aspects have received much attention, regrettably without any concern for the genetic architecture of its populations. The population structure in the central and eastern Mediterranean Sea (captures from six Italian and two Greek landings) has been analysed on the basis of surveys carried out with mitochondrial and AFLP markers. Data revealed the presence of a gradual discrepancy along a west–east axis. This species, occurring mainly at a depth of between 100 and 400 m, is not strongly confined in isolated demes, but it demonstrates an ‘Isolation By Distance’ model, within the Mediterranean Sea, which includes geographical areas with a some degree of isolation. The role of hydrodynamic forces, such as currents, water fronts, is discussed; and a further evidence of the ‘Levantine isolation’ within Mediterranean basin is shown.     

Investigating the molecular systematic relationships amongst selected Plesionika (Decapoda: Pandalidae) from the Northeast Atlantic and Mediterranean Sea

Despite the high number of species and ecological diversity of pandalid shrimps, there has been no previous attempt to resolve evolutionary relationships of several genera using molecular tools. Although mitochondrial DNA cytochrome oxidase I (COI) is widely used in barcoding studies to delimit species boundaries, additional insights into phylogenetic affinities can be obtained, especially when used in combination with data from additional genes. The knowledge of molecular diversity is essential to understand phylogenetic relationships and will help systematic clarifications. Based on partial fragments of the 16S and COI genes, we have focused specifically on addressing the systematic relationships of the economically and ecologically important shrimp genus Plesionika within a framework of five genera from within the Pandalidae. Our results showed that species within Plesionika are substantially divergent when compared with other genera, exhibiting the highest average nucleotide divergence, with 0.1123 and 0.0846 in COI and 16S genes, respectively. In addition, sequence divergence was found to vary greatly within the genus Plesionika (COI/16S): 0.0247/0.0016 between Plesionika antigai and Plesionika heterocarpus and 0.1616/0.098 between Plesionika heterocarpus and Plesionika edwardsii. We did not find amino acid sequence divergence between P. heterocarpus and P. antigai compared with P. heterocarpus and P. edwardsii (8.10%, K2P distance). Three species of Plesionika (P. antigai, P. heterocarpus and Plesionika scopifera) appear well separated from other Plesionika species in both maximum likelihood and Bayesian analyses. The present study confirms the utility of COI over 16S as a genetic marker to resolve relationships between different species of Plesionika from the Northeast Atlantic and Mediterranean Sea, in addition to species delimitation. The findings highlight the need to further review paraphyly within Plesionika in an attempt to recognize a concordance in the evolutionary history of Plesionika with major ecological and geological events.     

Deep‐water Corallium rubrum (L., 1758) from the Mediterranean Sea: preliminary genetic characterisation

The precious red coral Corallium rubrum (L., 1758) lives in the Mediterranean Sea and adjacent Eastern Atlantic Ocean on subtidal hard substrates. Corallium rubrum is a long‐lived gorgonian coral that has been commercially harvested since ancient times for its red axial calcitic skeleton and which, at present, is thought to be in decline because of overexploitation. The depth distribution of C. rubrum is known to range from c. 15 to 300 m. Recently, live red coral colonies have been observed in the Strait of Sicily at depths of c. 600–800 m. This record sheds new light on the ecology, biology, biogeography and dispersal mechanism of this species and calls for an evaluation of the genetic divergence occurring among highly fragmented populations. A genetic characterization of the deep‐sea red coral colonies has been done to investigate biological processes affecting dispersal and population resilience, as well as to define the level of isolation/differentiation between shallow‐ and deep‐water populations of the Mediterranean Sea. Deep‐water C. rubrum colonies were collected at two sites (south of Malta and off Linosa Island) during the cruise MARCOS of the R/V Urania. Collected colonies were genotyped using a set of molecular markers differing in their level of polymorphism. Microsatellites have been confirmed to be useful markers for individual genotyping of C. rubrum colonies. ITS‐1 and mtMSH sequences of deep‐water red coral colonies were found to be different from those found in shallow water colonies, suggesting the possible occurrence of genetic isolation among shallow‐ and deep‐water populations. These findings suggest that genetic diversity of red coral over its actual range of depth distribution is shaped by complex interactions among geological, historical, biological and ecological processes.     

Matrilineal evidence for genetic structure and Late Pleistocene demographic expansion of the Ornate goby Istigobius ornatus (Teleostei: Gobiidae) in the Persian Gulf and Oman Sea

The Persian Gulf and Oman Sea are characterized by an interesting paleoclimatic history and different ecological settings, and offer a unique study area to investigate the genetic structure of marine organisms including fishes. The Ornate goby Istigobius ornatus is widely distributed throughout the tropical Indo‐West Pacific including the Persian Gulf and Oman Sea. Here, we present the population structure, genetic diversity, and demographic history of four populations of I. ornatus from the latter two regions using the D‐loop marker of mitochondrial DNA. The results reveal a shallow genealogy, a star‐like haplotype network, significance of neutrality tests, and unimodal mismatch distribution. This is concordant with a recent demographic expansion of I. ornatus in the Persian Gulf and Oman Sea at about 63,000–14,000 years ago, which appears to be related to Late Pleistocene sea level fall and rise. The results of the pairwise Fst estimates imply high gene flow along the coast of the Persian Gulf, which is probably due to larval dispersion, whereas the Oman Sea population clearly differs from all Persian Gulf populations. The AMOVA result indicates that 7.74% of the variation is related to differences among ecoregions, while inter‐ and intra‐population differences explained ?3.20% and 95.47% of the variation, respectively. The haplotype network depicts two groups of haplotypes, most of them were specific to the Persian Gulf. No further evidence for geographic lineage substructuring was evident. The Mantel test result indicates that isolation by distance is not the main mechanism that promoted the genetic differentiation among the studied populations of I. ornatus. We suggest that cumulative effects of ecological and geographic barriers such as salinity, oceanographic conditions, and the presence of the Strait of Hormuz have shaped the genetic structure of I. ornatus in the Persian Gulf and Oman Sea.     

Feeding ecology of Ammothella longipes (Arthropoda: Pycnogonida) in the Mediterranean Sea: A fatty acid biomarker approach

Fatty acid analysis has proved valuable in determining seasonal trophic links and the feeding behavior in organisms in which these diet and trophic links cannot be inferred from stomach content analyses. Seasonal variations in total free fatty acid content (TFFA) and fatty acid composition of seston (<250 μm), the brown macroalgae Stypocaulon spp., polychaetes (Nereididae) and the pycnogonid Ammothella longipes have been used to establish their trophic links, with particular focus on seasonality and feeding ecology of A. longipes. Samples were collected in a coastal environment (NW Mediterranean Sea) at 7–10 m depth, in five different periods (August and October 2008, February, June and September 2009). Seston and Stypocaulon spp. samples did not show significant seasonal variations in TFFA content, while nereids showed a significant variation. Analysis of fatty acid profile showed high similarities of fatty acid composition between seston and Stypocaulon spp. Nereids were closer to seston and Stypocaulon spp. than A. longipes, which seemed to follow a seasonal trend. The results of this study reveal that A. longipes may change its feeding behavior depending on the season and available food. This pycnogonid species appears to be carnivore during spring and early summer but seems to feed on detritus when availability of prey diminishes during winter. Notable high amounts of odd-chain fatty acids are found in summer–autumn for this species, which may come from bacteria acquired from the detrital diet or from de novo biosynthesis from propionate. The results obtained provide new and valuable data on the understudied feeding biology of pycnogonids in general, and contribute to the understanding of their functioning of Mediterranean shallow oligotrophic systems and their trophic links.     

Transferable Fishing Concessions (TFC): A pilot study on the applicability in the Mediterranean Sea

Fisheries management systems based on Transferable Fishing Concessions (TFC) and similar rights-based systems have been developed during the last decades in some European countries. However, at present there is not a clear view on the possible effects caused by the application of this management systems in the Mediterranean Sea. The current study, involving nine Geographical Sub-Areas (GSAs) of the Mediterranean Sea, focuses on the appropriateness, transferability and modes of applicability of a TFC system in the Mediterranean area. Three different scenarios of quota allocation have been analyzed by taking into account biological, ecological, environmental, economic and social aspects: quota in terms of resource quantity, quota as a portion of the total fishing time, quota as a portion of the total fishing capacity. Results show that the transferability of a TFC-based system to the Mediterranean context appears to be low due to the characteristics of the Mediterranean fisheries (multispecificity of resources, fishing grounds shared among different countries, multigear, importance of small-scale fisheries) and to the general lack of sound and reliable individual historical data. The study also highlights rights-based systems such as Territorial Use Rights in Fisheries (TURF) might only be applied for the exploitation of sedentary resources, such as clams. A management system based on TFC could be theoretically reasonable for anchovy fishing, where a few species are caught, even if all countries and stakeholders should be involved in the decision making process.     

Eastern and Western Poor Cod (Trisopterus minutus capelanus) Populations in the Mediterranean Sea: Evidence from Allozyme and Minisatellite Loci

Abstract. Nine allozyme and two minisatellite loci were used to investigate potential genetic differentiation among three samples of Mediterranean poor cod, Trisopterus minutus capelanus, from the Gulf of Lion, the Tuscan Archipelago and the Aegean Sea. Both types of markers showed consistent results, with F_ST values of 0.0262 and 0.0296 (P < 0.0015, after Bonferroni correction for multiple tests) for allozymes and minisatellites, respectively. Allele frequency heterogeneity tests between pairs of samples showed a clear separation between the two western Mediterranean samples (Gulf of Lion, Tuscan Archipelago) and the eastern one (Aegean Sea). The results indicate that at least two reproductively isolated populations of poor cod occur in the Mediterranean.     

The Adaptive Marine Policy (AMP) toolbox: Supporting policy-makers developing adaptive policies in the Mediterranean and Black Sea

Adaptive management is essential to the practical application of the Ecosystem-Based Approach (EBA). Despite there are frequent assertions that adaptive management is being used, evidence on its success is still limited. Indeed, it is difficult to bring the different elements of adaptive management together in a robust way and to choose the appropriate tools to do it. Therefore, it is necessary to provide a practical framework for adaptive policy action, consistent with the EBA. Accordingly, to operationalize the design and implementation of adaptive policies on the basis of the EBA, the Adaptive Marine Policy toolbox has been developed. The objective of the toolbox is to provide policy-makers a practical framework to design and implement adaptive policies. To show the functionality of the toolbox, the guidelines and resources provided within the toolbox have been applied to the marine litter issue in the Mediterranean and Black Sea as an example. The example application has shown that the toolbox is a useful and operational framework to build a science-policy interface according to the EBA. Despite some resources could be missing from the toolbox, they provide a practical and useful starting point to support the application of the different steps and key activities.     

Microphytobenthic primary production as C uptake in sublittoral sediments of the Gulf of Trieste (northern Adriatic Sea): Methodological aspects and data analyses

From January 2003 to December 2004 microphytobenthic primary production was estimated both from in situ (MPPs) and in the laboratory (MPPp) ¹⁴C-incubation of slurries collected in a coastal site of the Gulf of Trieste (northern Adriatic Sea). MPPs values varied from −7.54 ± 3.12 to 34.59 ± 7.66 mg C m⁻² h⁻¹ over the whole period. The lowest MPPs were observed in November 2003 and August 2004, while the highest MPPs in July 2003 and May 2004, in correspondence with high PAR at the bottom. Significant correlations between MPPs and the microphytobenthic biomass (BIOM) (r = 0.75, p < 0.001), between MPPs and PAR at the bottom (r = 0.54, p < 0.01) and between MPPs and OXY (r = 0.50, p < 0.05) were revealed. MPPp values were higher than MPPs ones in 15 out of 23 observations, with the highest MPPp recorded in July 2003. At 17 m depth a seasonal pattern of sampling months was revealed by the cluster analysis. The role of abiotic parameters in determining this seasonal pattern was highlighted by the PCA, with the first axis correlated with MPPs and PAR, and the second one with temperature. Applying the fuzzy sets it resulted that spring months showed a higher degree of membership with MPPs, summer months with temperature and autumn–winter months with OXY. The microphytobenthic community did not seem to be photosynthetically active throughout the study period. From August–September to December low or negative MPPs values were recorded. We infer that during these months a shift from the autotrophic to heterotrophic metabolism of the benthic microalgae occurred in correspondence with low PAR and/or high temperature at the bottom. Despite the progressive lowering of the trophy of the study area occurred during the last 20 years, we found higher primary production values than those estimated two decades earlier.     

Long‐term comparison of structure and dynamics of the red coral metapopulation of the Portofino Promontory (Ligurian Sea): a case‐study for a Marine Protected Area in the Mediterranean Sea

A large amount of data on the precious coral Corallium rubrum has attested to a dramatic shift in the size structure of its over‐harvested Mediterranean populations in recent decades. One of the main problems for the conservation of this species is the substantial lack of data concerning the time span necessary for a population subjected to pluri‐decennial harvesting pressure to return to its pristine status. Here, we present a multi‐annual data set gathered from the Marine Protected Area (MPA) of Portofino, which hosts the most important shallow‐water coral populations in the Ligurian Sea and was subjected to strong harvesting pressure from the 1950s to the early 1970s. Quantitative comparison of the population structure data recorded in 1964, 1990 and 2012 indicated a strong size increase of the colonies (from 3 to 8 g mean weight), resulting in an increase in colony biomass from 300 to the current 1500 g·m^?2. As a consequence, over the same span of time, the density of colonies has slightly decreased. The role of mass mortality phenomena, like that occurred in this area during 1999, as possible biological features triggering the switch of red coral populations from a ‘grass plain‐like’ towards a ‘forest‐like’ structure, is discussed. All these data indicate that the instigation of MPAs is a winning strategy in the conservation of this precious species and similar management plans should also be evaluated for the protection of the deep benthic communities thriving on off‐shore banks.     

Spatio-temporal variations in reproductive patterns and population structure of Pasiphaea multidentata (Decapoda: Caridea) in the Blanes canyon and adjacent margin, North-western Mediterranean Sea

Pasiphaea multidentata is a deep‐water caridean shrimp fished in the Mediterranean in association with the commercially exploited red‐shrimp Aristeus antennatus. A previous study describes seasonality in the reproductive pattern of P. multidentata using external morphological parametres. This study assesses the spatio‐temporal variations in the population structure, sex ratio, ovary cycle and gametogenesis of P. multidentata from three different fishing grounds in the Blanes canyon and adjacent margin (North‐western Mediterranean) over an annual cycle. The oogenetic pattern of this species is typical of a caridean shrimp. There is a pool of previtellogenic oocytes at all times that develop from the periphery of the gonad towards the centre during maturation. Previtellogenic oocytes grow to approximately 200 μm before undergoing vitellogenesis. The vitellogenic oocytes are surrounded by a monolayer of accessory cells. The maximum size observed for a mature oocyte was 1420 μm. The oocyte‐size distribution confirmed the seasonal reproductive pattern of this species; in winter, the ovaries contained mainly previtellogenic oocytes, some of which start maturing in spring, resulting in a slightly bimodal distribution. In summer, the vitellogenic oocytes reach approximately 1000 μm and in late autumn the ovaries are fully mature and ready to spawn. There were no significant differences in the reproductive and population structure patterns of P. multidentata among the three sites, suggesting that the population’s distribution is not affected by the geomorphology of the area, in particular the presence of the canyon. The populations are dominated by females at all sites and all seasons, with the arrival of juveniles in spring. The seasonal variations in the reproduction and recruitment of P. multidentata and the lack of spatial segregation within the population are discussed in terms of the species’ known biology, the effects of canyons in energy supply to the deep‐sea floor and the relationships of this species with the red‐shrimp A. antennatus.     

Midlittoral polychaete communities in the Eastern Mediterranean Sea: new information from the implementation of the Natural Geography in Shore Areas (NaGISA) protocol and comparisons at local and regional scales

The aim of this study was to attempt to fill current knowledge gaps on midlittoral Mediterranean biodiversity at local and regional scales, by using benthic polychaetes as a model taxon. Two different data sets were analysed: (i) a quantitative data set from the two Natural Geography in Shore Areas (NaGISA) study sites in Crete and (ii) a qualitative data set from multiple sites across the Mediterranean. At the local scale, the results provide evidence that (i) discrete species communities are formed in midlittoral Mediterranean habitats, which vary by geographical location and year, depending on the scale of observation; (ii) macrophyte coverage and Chl‐a are the only environmental variables associated, albeit weakly, with the above pattern; (iii) although naturally disturbed, the Cretan NaGISA sites do not seem to experience any anthropogenic stress; (iv) environmental heterogeneity and history seem to be much less important in shaping the polychaete communities than inter‐specific interactions; however, it is not possible to specify at this stage whether local or regional processes or even their interactions may shape the polychaete communities. At the regional scale, the results indicate that (i) the only factor that seems to be involved in the regional pattern is the identity of the study providing the data sets, which implies variability and bias in how research projects are carried out, from the sampling design through to data collection and analysis; (ii) the Cretan NaGISA sites may be considered as representative of the habitat in the Mediterranean, under certain conditions.     

Ontogenetic shifts and temporal changes in the trophic patterns of the deep‐sea red shrimp,Aristaeomorpha foliacea (Decapods: Aristeidae), in the Eastern Ionian Sea (Eastern Mediterranean)

The purpose of this paper is to provide the first detailed data concerning the diet and feeding activity of the giant red shrimp, Aristaeomorpha foliacea, in the Eastern Ionian Sea (Eastern Mediterranean), in relation to season, size class and sex. Feeding activity in A. foliacea was intense, based on its low vacuity index and high prey diversity, with a diet dominated by mesopelagic prey and less frequent occurrence of benthic taxa. Giant red shrimp displayed a highly diversified diet that exhibited slight seasonal fluctuations. The diets of both sexes consisted of 60 different prey categories belonging chiefly to three groups: crustaceans (e.g. decapods, such as Plesionika spp. and Pasiphaeidae, amphipods), cephalopods (mainly Enoploteuthidae) and fishes (Myctophidae, Macrouridae). These three prey categories accounted for 72–82% of the relative abundance and total occurrence for males and 70–88% for females, respectively. Variation in food availability, as well as increased energy demands related to gonad development and breeding activity, appear to be critical factors driving temporal changes in feeding strategy. Feeding activity increased during spring and summer, which coincides with reproductive activities (mating, gonad maturation, egg‐laying). Females seem to be more active predators than males, consuming prey with greater swimming ability. However, ontogenetic shifts in diet were also apparent, despite high dietary overlap among small, medium and large females. Large individuals, which are more efficient predators, selected highly mobile prey (e.g. fishes), whereas small individuals consumed low‐mobility prey (e.g. copepods, ostracods, tanaids and sipunculans).