Paola Nisi Cerioni

A centromeric satellite DNA may be involved in heterochromatin compactness in gobiid fishes.

Centromere and telomere composition and organization were studied in various gobiid species exhibiting and not exhibiting chromosome polymorphisms involving Robertsonian rearrangements. In Gobius cobitis, we isolated an AT-rich centromeric DNA satellite, designated pCOB, and found that several sequences contain adenine stretches, various CA/TG dinucleotide steps, and a sequence 76% homologous to the yeast CDE III centromeric sequence. All of these traits are generally considered important for centromeric function, and the hypothesis has been advanced that some are involved in the control of DNA curvature and thus in the degree of centromeric chromatin compactness. Based on these features, and on the fact that they are found only in the species not exhibiting Robertsonian biarmed chromosomes, a role for pCOB in preventing centric fusions has been hypothesized. Our data also suggest that, as in other species, the formation of Robertsonian biarmed chromosomes is accompanied by the loss of telomeric sequences.

A satellite DNA containing CENP-B box-like motifs is present in the Antarctic scallop Adamussium colbecki

The DNA of the Antarctic scallop Adamussium colbecki was found to contain a highly repeated sequence identifiable upon restriction with endonuclease BglII. The monomeric unit - denominated pACS (about 170bp long) - was cloned. Southern blot hybridization yielded a ladder-like banding pattern, indicating that the repeated elements are tandemly arranged in the genome and therefore represent a sequence of satellite DNA. Sequence analysis of five different clones revealed the presence of various subfamilies, some of which showed a high degree of divergence. In each clone, regions homologous to the mammalian CENP-B box were observed. A region homologous to the CDEIII centromeric sequence of yeast was also found in one of the clones. These observations suggest a relationship of the pACS family to the centromeric area in A. colbecki.

Phylogeographic inferences on the native brown trout mtDNA variation in central Italy

Genetic diversity was analysed in Salmo trutta populations living in an area of central Italy by sequencing 310 bp of the 5′ end of the mtDNA control region (D‐loop) and by Restriction Fragment Length Polymorphism (RFLP) analysis of three mtDNA segments. Data show a genetic structure profoundly altered by stockings with allochthonous material of Atlantic origin. In fact, 15 of the RFLP haplotypes detected are linked to an Atlantic sequence. The remaining 9 were instead coupled with sequences representing the three major phylogenetic lineages previously identified in the Mediterranean basin (Adriatic, marmoratus, and Mediterranean), representing the native genetic diversity of brown trout in that area. The close genetic affinity observed between these latter haplotypes and those found in the Balkan peninsula by other authors seems to be in accordance with a recent, natural, history of dispersion between the two borders of the Adriatic Sea. These results appear significant from a conservation point of view as, in spite of the massive stocking with hatchery‐reared specimens, they highlight the persistence of Salmo trutta native genetic diversity in central Italy.

Genetic characterization of loggerhead turtle ( Caretta caretta ) individuals stranded and caught as bycatch from the North-Central Adriatic Sea

The North Adriatic Sea is considered a critical feeding and developmental area for Mediterranean loggerhead turtles. In this study, a comparative analysis of mitochondrial DNA control region sequences was carried out on sixty-five loggerhead individuals stranded and caught as bycatch in the Adriatic Sea from 1999 to 2002. We demonstrated the existence of genetic relationships between the North-Central Adriatic (NCA) aggregate and the Central-Eastern Mediterranean rookeries. Short-range and long-range migrations towards the Adriatic Sea were hypothesized by the finding of individuals bearing haplotypes endemic to the nesting populations of Greece and Turkey. The occurrence of individuals belonging to dimensional classes from juveniles to mature adults strongly support both the feeding and developmental role of the NCA.

A molecular analysis of the systematics of three Antarctic bivalves

Abstract In this paper we performed a molecular analysis of the systematics of three Antarctic bivalve species: Adamussium colbecki, Laternula elliptica, and Yoldia eightsi. The taxonomic position of A. colbecki, that is included in the family Pectinidae by some Authors, and in Propeamussiidae by others, was studied by analysing 18S rDNA, mitochondrial 12S, 16S rDNA. The results showed that A. colbecki belongs to Pectinidae. No element of evidence supports the inclusion of A. colbecki in any other family. Also studied in this species was a repetitive DNA sequence which shows characters typical of the centromeric DNAs found in many other eukariotes. In the other two Antarctic species, we investigated only 18S rDNA and compared it with the sequences published in the literature of species belonging to various bivalve subclasses. These molecular data suggest that the subclass to which Y. eightsi belongs is primitive, and that L. elliptica, which is usually placed among Anomalodesmata, shows a close relationship with Heterodonta.

Isolation and Characterization of Two Satellite DNAs in some Iberian Rock Lizards (Squamata, Lacertidae)

Satellite DNAs represent a large portion of all high eukaryotic genomes. They consist of numerous very similar repeated sequences, tandemly arranged in large clusters up to 100 million base pairs in length, usually located in the heterochromatic parts of chromosomes. The biological significance of satDNAs is still under discussion, but most of their proposed functions are related to heterochromatin and/or centromere formation and function. Because information about the structure of reptilian satDNA is far from exhaustive, we present a molecular and cytogenetic characterization of two satDNA families in four lacertid species. Two families of tandemly repeated DNAs, namely TaqI and HindIII satDNAs, have been cloned and sequenced from four species belonging to the genus Iberolacerta. These satDNAs are characterized by a monomer length of 171-188 and 170-172 bp, and by an AT content of 60.5% and 58.1%, respectively. FISH experiments with TaqI satDNA probe produced bright signals in pericentromeric regions of a subset of chromosomes whereas all the centromeres were marked by HindIII probe. The results obtained in this study suggest that chromosome location and abundance of satDNAs influence the evolution of these elements, with centromeric families evolving tenfold faster than interstitial/pericentromeric ones. Such different rates render different satellites useful for phylogenetic investigation at different taxonomic ranks.

Evolutionary dynamics of two satellite DNA families in rock lizards of the genus Iberolacerta (Squamata, Lacertidae): different histories but common traits.

Satellite DNAs compose a large portion of all higher eukaryotic genomes. The turnover of these highly repetitive sequences is an important element in genome organization and evolution. However, information about the structure and dynamics of reptilian satellite DNA is still scarce. Two satellite DNA families, HindIII and TaqI, have been previously characterized in four species of the genus Iberolacerta. These families showed different chromosomal locations, abundances, and evolutionary rates. Here, we extend the study of both satellite DNAs (satDNAs) to the remaining Iberolacerta species, with the aim to investigate the patterns of variability and factors influencing the evolution of these repetitive sequences. Our results revealed disparate patterns but also common traits in the evolutionary histories of these satellite families: (i) each satellite DNA is made up of a library of monomer variants or subfamilies shared by related species; (ii) species-specific profiles of satellite repeats are shaped by expansions and/or contractions of different variants from the library; (iii) different turnover rates, even among closely related species, result in great differences in overall sequence homogeneity and in concerted or non-concerted evolution patterns, which may not reflect the phylogenetic relationships among taxa. Contrasting turnover rates are possibly related to genomic constraints such as karyotype architecture and the interspersed organization of diverging repeat variants in satellite arrays. Moreover, rapid changes in copy number, especially in the centromeric HindIII satDNA, may have been associated with chromosomal rearrangements and even contributed to speciation within Iberolacerta.

Slow evolving satellite DNAs: the case of a centromeric satellite in Chalcides ocellatus (Forskål, 1775) (Reptilia, Scincidae)

Satellite DNAs represent a preponderant portion of eukaryotic genomes, and despite the ample literature on satDNAs of eukaryotes little is known about these repetitive elements in reptiles. Studies on reptiles satellite DNAs have been mainly focused on lacertid lizards and only one aimed at characterising these repetitive elements in skinks. Here, the isolation and characterisation of a satellite DNA in two populations of the ocellated skink, Chalcides ocellatus (Forskal, 1775), is presented. The repetitive element isolated is located at centromeres of all chromosomes of the complement, shows a tendency towards AT enrichment (53.5%), and contains short motifs that are common in centromeric satellites of eukaryotes (TG/CA, GAAA). The satellite shows an extremely low evolutionary rate (0.13% per million year) that make it unsuitable as a phylogenetic probe to assess the genetic differentiation of the populations investigated, that show a deep genetic divergence at mitochondrial level. The influence of satellite location on chromosomes and chromosomal morphology are invoked to explain this unusually slow mutation rate.

Chromosomal study of a lamprey (Lampetra zanandreai Vladykov, 1955) (Petromyzonida: Petromyzontiformes): conventional and FISH analysis

Karyotype and other chromosomal characteristics in the Adriatic brook lamprey Lampetra zanandreai, representative of one of the most ancestral group of vertebrates, were examined using conventional (Ag-staining, C-banding as well as CMA3 and DAPI fluorescence) and molecular (FISH with 18/28S rDNA and EcoRI satDNA as probes) protocols with metaphase chromosomes derived from whole blood cultures. The chromosome complement had a modal diploid chromosome number of 2n = 164, as in other petromyzontid lamprey species. Ag-staining and CMA3 fluorescence, as well as FISH with 18/28S rDNA probes, detected nucleolar organizer regions (NORs) close to the centromeres of the biarmed chromosomes of pairs 1 and 2, the largest chromosome pairs of the complement. In addition to NORs, CMA3 fluorescence revealed positive signals in approximately 40 other chromosomes. DAPI stained mostly centromeric regions of many chromosomes as well as conspicuously massive blocks overlapping NOR sites. C-banding evidenced a large amount of constitutive heterochromatin in somatic chromosomes, with approximately 40 C-positive acrocentric elements completely heterochromatic, corresponding with the 40 CMA3+ chromosomes and positive heterochromatic blocks in pericentromeric regions of chromosome pairs 1 and 2. Polymerase chain reaction (PCR)-based cloning of satellite DNA with primers derived from Petromyzon marinus centromeric sequences was successful for L. zanandreai genomic DNA. The sequence was AT-rich (59%) and characterized by short consensus motifs similar to other centromeric satellite motifs. FISH using satDNA clones as a probe produced a fluorescent signal on a single pair of small chromosomes. This sequence was PCR-amplified also in L. planeri and P. marinus genomic DNA, and the evolution of this repetitive element in the above species was analysed.

Coupling Demographic and Genetic Variability from Archived Collections of European Anchovy (Engraulis encrasicolus)

It is well known that temporal fluctuations in small populations deeply influence evolutionary potential. Less well known is whether fluctuations can influence the evolutionary potentials of species with large census sizes. Here, we estimated genetic population parameters from as survey of polymorphic microsatellite DNA loci in archived otoliths from Adriatic European anchovy (Engraulis encrasicolus), a fish with large census sizes that supports numerous local fisheries. Stocks have fluctuated greatly over the past few decades, and the Adriatic fishery collapsed in 1987. Our results show a significant reduction of mean genetic parameters as a consequence of the population collapse. In addition, estimates of effective population size (Ne) are much smaller than those expected in a fishes with large population census sizes (Nc). Estimates of Ne indicate low effective population sizes, even before the population collapse. The ratio Ne/Ne ranged between 10−6 and 10−8, indicating a large discrepancy between the anchovy gene pool and population census size. Therefore, anchovy populations may be more vulnerable to fishery effort and environmental change than previously thought.