Gian Luca Dedola

Mitochondrial DNA reveals genetic structuring of Pinna nobilis across the Mediterranean Sea.

Pinna nobilis is the largest endemic Mediterranean marine bivalve. During past centuries, various human activities have promoted the regression of its populations. As a consequence of stringent standards of protection, demographic expansions are currently reported in many sites. The aim of this study was to provide the first large broad-scale insight into the genetic variability of P. nobilis in the area that encompasses the western Mediterranean, Ionian Sea, and Adriatic Sea marine ecoregions. To accomplish this objective twenty-five populations from this area were surveyed using two mitochondrial DNA markers (COI and 16S). Our dataset was then merged with those obtained in other studies for the Aegean and Tunisian populations (eastern Mediterranean), and statistical analyses (Bayesian model-based clustering, median-joining network, AMOVA, mismatch distribution, Tajima’s and Fu’s neutrality tests and Bayesian skyline plots) were performed. The results revealed genetic divergence among three distinguishable areas: (1) western Mediterranean and Ionian Sea; (2) Adriatic Sea; and (3) Aegean Sea and Tunisian coastal areas. From a conservational point of view, populations from the three genetically divergent groups found may be considered as different management units.

Patterns of spatial genetic structuring in the endangered limpet Patella ferruginea: implications for the conservation of a Mediterranean endemic

Patella ferruginea Gmelin, 1791 is an endangered marine gastropod endemic to the Western Mediterranean. Its range is restricted to the Sardinian-Corsican region (SCR), North Africa, a few scattered sites in Southern Spain, and Sicily. Inter-simple sequence repeat (ISSR) markers and three different mitochondrial DNA (mtDNA) regions, Cytochrome c Oxidase subunit I, 12S (small-subunit ribosomal RNA gene) and 16S (large-subunit ribosomal RNA gene), were used to investigate the presence of genetic population structuring. The mtDNA sequences showed very low levels of genetic differentiation. Conversely, ISSRs showed the presence of two main genetic groups, corresponding to Spain, North Africa and Sicily and the SCR. The SCR was further split into two subgroups. The ISSR results suggest that, on a regional scale, the genetic structure of P. ferruginea is mainly determined by the restriction of gene flow by dispersal barriers. On a more local scale human harvesting may play a crucial role in population structuring by increasing the effect of genetic drift.

PCR-RFLP: a practical method for the identification of specimens of Patella ulyssiponensis s.l. (Gastropoda: Patellidae )

Abstract Patella ulyssiponensis s.l. is widely distributed in the Mediterranean as well as in the north-eastern Atlantic, from southern Norway to north-western Africa, including Macaronesia. Throughout its range, P. ulyssiponensis s.l. shows a high degree of variability in the shape and colour pattern of the shell and in the colour pattern of the foot. In addition, the species demonstrates widely overlapping morphological parameters with the coexisting P. caerulea (in the Mediterranean), P. vulgata (in north-eastern Atlantic) and P. candei (in the Macaronesian islands). Thus P. ulyssiponensis s.l. identification proves to be difficult. So far, method to unequivocally identify uncertain specimens of P. ulyssiponensis s.l. from the coexisting species was using a molecular taxonomy approach based on the Cytochrome c Oxidase subunit I (COI) sequences analysis. The aim of the present study was to identify specific PCR-RFLP (Restriction Fragment Length Polymorphism PCR-based) markers on the COI sequences which could be used as an alternative and fast diagnostic tool for the discrimination of P. ulyssiponensis s.l. from P. caerulea, P. vulgata and P. candei, when the morphology of the coexisting individuals provided equivocal information. First, we sampled 65 Patella spp. and classified these by means of the COI sequencing. Then, we selected the TaqI endonuclease for the specific RFLP reaction, which produced a combination of RFLP electrophoretic bands, allowing an unequivocal identification of the individuals of P. ulyssiponensis s.l.

Patterns of spatial genetic variation in Patella ulyssiponensis: insights from the western Mediterranean marine ecoregion

Patterns of genetic variation in marine species reflect the interplay of species-specific traits, oceanographic features, historical processes and selection. In the Atlantic–Mediterranean regions, Patella ulyssiponensis (Mollusca: Gastropoda) was previously used as a model to investigate these patterns. Our study gained insight into the genetic patterns of P. ulyssiponensis in the western Mediterranean marine ecoregion (WME), by means of ISSRs and COI. We evaluated the genetic structure of the WME with respect to the Atlantic and eastern Mediterranean, as well as the occurrence of further structuring within this ecoregion. Both population- and individual-based analysis evidenced that WME does not appear to be sharply isolated from the adjacent regions. Within the WME, P. ulyssiponensis displays a pattern of genetic structure that may reflect a chaotic patchiness scenario: structuring is neither related to coastal distance nor to other factors that may constrain dispersal. Compared to the congener P. ferruginea, P. ulyssiponensis shows weaker spatial genetic structure, which may reflect a higher dispersal potential coupled with greater population effective size. Whilst other processes that may have influenced the genetic pattern in the WME remain to be cleared, a recent range expansion coupled with species-specific traits favouring larval dispersal may have contributed to the genetic structuring.

Mendelian breeding units versus standard sampling strategies: mitochondrial DNA variation in southwest Sardinia

We report a sampling strategy based on Mendelian Breeding Units (MBUs), representing an interbreeding group of individuals sharing a common gene pool. The identification of MBUs is crucial for case-control experimental design in association studies. The aim of this work was to evaluate the possible existence of bias in terms of genetic variability and haplogroup frequencies in the MBU sample, due to severe sample selection. In order to reach this goal, the MBU sampling strategy was compared to a standard selection of individuals according to their surname and place of birth. We analysed mitochondrial DNA variation (first hypervariable segment and coding region) in unrelated healthy subjects from two different areas of Sardinia: the area around the town of Cabras and the western Campidano area. No statistically significant differences were observed when the two sampling methods were compared, indicating that the stringent sample selection needed to establish a MBU does not alter original genetic variability and haplogroup distribution. Therefore, the MBU sampling strategy can be considered a useful tool in association studies of complex traits.

COI sequencing as tool for the taxonomic attribution of Patella spp. (Gastropoda): the case of morphologically undistinguishable juveniles settled on a Patella ferruginea adult

Patella ferruginea is an endangered marine gastropod, distributed on the western Mediterranean coasts, whose range has progressively contracted, due to intense human exploitation. A genetic analysis was performed on two unidentified young individuals belonging to the genus Patella found attached to the shell of an adult of P. ferruginea , with a twofold aim: (i) to achieve their correct taxonomic attribution by means of the DNA barcoding; and (ii) to shed some light on the hypothesized larval philopatry and/or juveniles phoresis in P. ferruginea . The survey was carried out comparing the sequences of the cytochrome c oxidase subunit I (COI) Folmer region obtained for the two juveniles with those obtained for adults of P. ferruginea , P. caerulea , P. rustica , and P. ulyssiponensis , from different sites of the western Mediterranean, by means of maximum likelihood cluster analysis and a Bayesian-based assignment test. Results obtained evidenced that: (i) COI may be used with confidence as DNA barcoding in the genus Patella ; and (ii) the two juveniles studied are not conspecific: one belonged to P. ferruginea , the other to P. rustica . The latter finding raises doubts about the juvenile phoresis and about the occurrence of larval philopatry in P. ferruginea , suggesting that an extensive use of a molecular approach for a better evaluation of the recruitment features of this endangered species should be adopted.

Cytochrome c oxidase subunit I variability in Ruditapes decussatus (Veneridae) from the western Mediterranean

Abstract Ruditapes decussatus (Linnaeus, 1758) (Veneridae) is an Atlanto-Mediterranean bivalve whose populations have experienced reductions and, in some instances, hybridisation with allochthonous R. philippinarum. Acquisition of additional genetic knowledge concerning the present R. decussatus populations is essential to address adequate conservation plans for this species. For this purpose, we analysed a portion of the mtDNA cytochrome c oxidase subunit I (COI) region in populations from the western Mediterranean, where this species represents a harvested fishery resource. Our analyses revealed an overall lack of genetic structure within the western Mediterranean area, and the occurrence of mtDNA substructuring between the Aegean and Marmara seas and the remaining populations from the whole Mediterranean basin and the South European Atlantic coast. The results obtained for populations from Sardinia, where extensive restocking programmes have not been reported and where R. philippinarum is rare and localised, suggest that intensive harvesting and potential dispersal alone may have been able to shape the genetic variation identified in the local R. decussatus populations.

Evolution of satellite DNA sequences in two tribes of Bovidae: A cautionary tale.

Abstract Two clones, Bt1 from Bos taurus and Om1 from Ovis orientalis musimon, were used as probes for hybridization on genomic DNA and on metaphase chromosomes in members of Bovini and Caprini tribes. Bt1 and Om1 are sequences respectively belonging to the 1.715 and 1.714 DNA satellite I families. Southern blots and fluorescence in situ hybridization experiments showed completely coherent results: the Bovini probe Bt1 hybridized only to members of the Bovini tribe and not to members of Caprini. Likewise, the Caprini probe Om1 hybridized only to members of the Caprini tribe and not to members of Bovini. Hybridization signals were detected in the heterochromatic regions of every acrocentric autosome, except for two pairs of autosomes from Capra hircus that did not show hybridization to probe Om1. No signal was detected on X and Y chromosomes or on bi-armed autosomes. Remarkably, probe Om1 showed almost 100% homology with a bacterial sequence reported in Helicobacter pylori.